Ubiquitin-protein ligase E3 Mdm2
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count | Chain A； UniProt 25–109 Chain B； UniProt 25–109 Chain C； UniProt 25–109 | Fragment：RESIDUES 25-109 Mutation：L33E | IMZ CIS-[4,5-BIS-(4-BROMOPHENYL)-2-(2-ETHOXY-4-METHOXYPHENYL)-4,5-DIHYDROIMIDAZOL-1-YL]-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]METHANONE × 5 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；278 K；54% SATD, AMMONIUM SULFATE, 2.5% PEG 200, 50mM GLUCOSE, 5mM DTT, 100mM TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K | Resolution 2.30 Å R-free 0.322 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 1RV1 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1T4E Structure of Human MDM2 in complex with a Benzodiazepine Inhibitor Deposited 2004-04-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
17–111（95 aa）
Fragment：p53-binding domain
Chain B
17–111（95 aa）
Fragment：p53-binding domain
|
Mutation：17-111, additional GLY at N-terminus Mutation：17-111, additional GLY at N-terminus | DIZ (4-CHLOROPHENYL)[3-(4-CHLOROPHENYL)-7-IODO-2,5-DIOXO-1,2,3,5-TETRAHYDRO-4H-1,4-BENZODIAZEPIN-4-YL]ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；(NH4)2SO4, PEG400, NaSCN, pH 6.5, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.60 Å R-free 0.276 |
| 1T4F Structure of human MDM2 in complex with an optimized p53 peptide Deposited 2004-04-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain M
17–125（109 aa）
|
Mutation：17-125, additional Gly at N-terminus | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；277 K；(NH4)2SO4, Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.231 |
| 1YCR MDM2 BOUND TO THE TRANSACTIVATION DOMAIN OF P53 Deposited 1996-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–125（109 aa）
Fragment：RESIDUES 17 - 125
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.60 Å R-free 0.276 |
| 1Z1M NMR structure of unliganded MDM2 Deposited 2005-03-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–118（118 aa）
Fragment：N-terminal domain
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.3
NMR sample composition
0.5mM HDM2(1-118), 60mM deuterated sodium acetate, 60mM phosphate buffer | 90% H2O/10% D2O
NMR sample composition
0.5mM HDM2(1-118), 60mM deuterated sodium acetate, 60mM phosphate buffer | 99.5% D2O
|
Resolution not provided |
| 2C6A Solution structure of the C4 zinc-finger domain of HDM2 Deposited 2005-11-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
290–335（46 aa）
|
Not recorded | ZN ZINC ION × 1 |
SOLUTION NMR
NMR measurement conditions
pH 6.5；293 K；Ionic strength (raw mmCIF value) 100
NMR sample composition
90% WATER/10% D2O
|
Resolution not provided |
| 2C6B Solution structure of the C4 zinc-finger domain of HDM2 Deposited 2005-11-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
290–335（46 aa）
|
Not recorded | ZN ZINC ION × 1 |
SOLUTION NMR
NMR measurement conditions
pH 6.5；293 K；Ionic strength (raw mmCIF value) 100
NMR sample composition
90% WATER/10% D2O
|
Resolution not provided |
| 2F1Y Crystal structure of the TRAF-like domain of HAUSP/USP7 bound to a MDM2 peptide Deposited 2005-11-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
224–232（9 aa）
Fragment：HAUSP N-terminal domain with MDM2 peptide fused to its C-terminal
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；26% PEG4000, 300 mM calcium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.237 |
| 2GV2 MDM2 in complex with an 8-mer p53 peptide analogue Deposited 2006-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–125（109 aa）
Fragment：p53 binding domain (Residues: 17-125)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9.5；298 K；2 M (NH4)2SO4, 100 mM Bicine, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.80 Å R-free 0.219 |
| 2HDP Solution Structure of Hdm2 RING Finger Domain Deposited 2006-06-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
429–491（63 aa）
Fragment：RING finger domain
Chain B
429–491（63 aa）
Fragment：RING finger domain
|
Not recorded | ZN ZINC ION × 4 |
SOLUTION NMR
NMR measurement conditions
pH 7.1；298 K；Ionic strength (raw mmCIF value) 0.15 M NaCl；Pressure ambient
NMR sample composition
0.1 mM Hdm2 RING domain, U-15N, 20 mM Tris, pH 7.1, 0.15M NaCl, 0.25M Arg, 0.5 mM TCEP, 5 uM ZnSO4, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
0.1 mM Hdm2 RING domain, U-15N,13C, 20 mM Tris, pH 7.1, 0.15M NaCl, 0.5 mM TCEP, 5 uM ZnSO4, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
0.1 mM Hdm2 RING domain, unlabled | 20 mM Tris, pH 7.1, 0.15M NaCl, 0.5 mM TCEP, 5 uM ZnSO4, 90% H2O, 10% D2O
|
Resolution not provided |
| 2LZG NMR Structure of Mdm2 (6-125) with Pip-1 Deposited 2012-10-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–125（125 aa）
|
Not recorded | 13Q [(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-(cyclopropylmethyl)-2-oxopiperidin-3-yl]acetic acid × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7；288.15 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition
500 uM [U-100% 13C; U-100% 15N] protein, 50 mM sodium chloride, 20 mM sodium phosphate, 5 mM [U-100% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2M86 Solution structure of Hdm2 with engineered cyclotide Deposited 2013-05-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
17–125（109 aa）
Fragment：UNP residues 17-125
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；300 K；Ionic strength (raw mmCIF value) 0.133；Pressure ambient
NMR sample composition
0.2 mM MCo-PMI, 0.2 mM [U-99% 13C; U-99% 15N] Hdm2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.2 mM [U-99% 15N] Mo-PMI, 0.2 mM Hdm2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.2 mM MCo-PMI, 0.2 mM Hdm2, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2MPS Structure of complex of MDM2(3-109) and P73 TAD(10-25) Deposited 2014-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
3–109（107 aa）
Fragment：UNP residues 3-109
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；283 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition
0.9 mM [U-99% 13C; U-99% 15N] E3 Ubiquitin-protein Ligase MDM2-1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.9 mM [U-99% 13C; U-99% 15N] Tumor protein P73-2, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2RUH Chemical Shift Assignments for MIP and MDM2 in bound state Deposited 2014-06-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
6–102（97 aa）
Fragment：MIP-MDM2 fusion, UNP residues 6-120
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.6；298 K；Ionic strength (raw mmCIF value) 160；Pressure ambient
NMR sample composition
650 uM [U-100% 13C; U-100% 15N] MIP-MDM2 fusion-1, 20 mM TRIS-2, 300 mM sodium chloride-3, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 2VJE Crystal Structure of the MDM2-MDMX RING Domain Heterodimer Deposited 2007-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
383–446（64 aa）
Fragment：RESIDUES 383-446
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；1.8 M NH4(SO4)2, 0.5 M NACL, 0.1 M NA CITRATE, PH 6.5
|
Resolution 2.20 Å R-free 0.223 |
| 2VJE Crystal Structure of the MDM2-MDMX RING Domain Heterodimer Deposited 2007-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
383–446（64 aa）
Fragment：RESIDUES 383-446
|
Not recorded | ZN ZINC ION × 4 FLC CITRATE ANION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；1.8 M NH4(SO4)2, 0.5 M NACL, 0.1 M NA CITRATE, PH 6.5
|
Resolution 2.20 Å R-free 0.223 |
| 2VJF Crystal Structure of the MDM2-MDMX RING Domain Heterodimer Deposited 2007-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
383–446（64 aa）
Fragment：RESIDUES 383-446
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；1.8 M NH4(SO4)2, 0.5 M NACL, 0.1 M NA CITRATE, PH 6.5
|
Resolution 2.30 Å R-free 0.234 |
| 2VJF Crystal Structure of the MDM2-MDMX RING Domain Heterodimer Deposited 2007-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
383–446（64 aa）
Fragment：RESIDUES 383-446
|
Not recorded | ZN ZINC ION × 4 FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；1.8 M NH4(SO4)2, 0.5 M NACL, 0.1 M NA CITRATE, PH 6.5
|
Resolution 2.30 Å R-free 0.234 |
| 3EQS Crystal structure of human MDM2 in complex with a 12-mer peptide inhibitor Deposited 2008-10-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
25–109（85 aa）
Fragment：UNP residues 25-109
|
Not recorded | GAI GUANIDINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；0.2 M Ammonium acetate, 0.1M Sodium citrate, 30% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.65 Å R-free 0.193 |
| 3EQS Crystal structure of human MDM2 in complex with a 12-mer peptide inhibitor Deposited 2008-10-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
25–109（85 aa）
Fragment：UNP residues 25-109
|
Not recorded | GAI GUANIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；0.2 M Ammonium acetate, 0.1M Sodium citrate, 30% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.65 Å R-free 0.193 |
| 3G03 Structure of human MDM2 in complex with high affinity peptide Deposited 2009-01-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
18–125（108 aa）
Fragment：N-terminal p53 binding domain, UNP residues 18-125
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；290 K；0.1M TRIS-HCl, 0.2M Ammonium Sulphate, pH7.5, 28% PEG5000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 290K
|
Resolution 1.80 Å R-free 0.268 |
| 3G03 Structure of human MDM2 in complex with high affinity peptide Deposited 2009-01-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
18–125（108 aa）
Fragment：N-terminal p53 binding domain, UNP residues 18-125
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；290 K；0.1M TRIS-HCl, 0.2M Ammonium Sulphate, pH7.5, 28% PEG5000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 290K
|
Resolution 1.80 Å R-free 0.268 |
| 3IUX Crystal structure of human MDM2 in complex with a potent miniature protein inhibitor (18-residues) Deposited 2009-08-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
25–109（85 aa）
Fragment：UNP residues 25-109, p53 binding domain, SWIB domain
|
Not recorded | ACT ACETATE ION × 3 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；273 K；2% PEG 400, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 1.65 Å R-free 0.206 |
| 3IUX Crystal structure of human MDM2 in complex with a potent miniature protein inhibitor (18-residues) Deposited 2009-08-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
25–109（85 aa）
Fragment：UNP residues 25-109, p53 binding domain, SWIB domain
|
Not recorded | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；273 K；2% PEG 400, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 1.65 Å R-free 0.206 |
| 3IWY Crystal structure of human MDM2 complexed with D-peptide (12 residues) Deposited 2009-09-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
25–109（85 aa）
Fragment：UNP residues 25-109, SWIB domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；273 K；0.05 M potassium phosphate monobasic, 20% PEG 8,000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 1.93 Å R-free 0.259 |
| 3IWY Crystal structure of human MDM2 complexed with D-peptide (12 residues) Deposited 2009-09-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
25–109（85 aa）
Fragment：UNP residues 25-109, SWIB domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；273 K；0.05 M potassium phosphate monobasic, 20% PEG 8,000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 1.93 Å R-free 0.259 |
| 3JZK crystal structure of MDM2 with chromenotriazolopyrimidine 1 Deposited 2009-09-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：MDM2 N-terminal domain, residues 17-111
|
Not recorded | YIN (6R,7S)-6,7-bis(4-bromophenyl)-7,11-dihydro-6H-chromeno[4,3-d][1,2,4]triazolo[1,5-a]pyrimidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；2.4 M (NH4)2SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.10 Å R-free 0.320 |
| 3JZR Human MDM2 liganded with a 12mer peptide inhibitor (pDI6W) Deposited 2009-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–125（109 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；2.2 M DL-Malic acid, 100 mM Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.10 Å R-free 0.228 |
| 3JZS Human MDM2 liganded with a 12mer peptide inhibitor (pDIQ) Deposited 2009-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
24–109（86 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；30% PEGmme2000, 100 mM Tris HCl, 200 mM MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 1.78 Å R-free 0.253 |
| 3LBK Structure of human MDM2 protein in complex with a small molecule inhibitor Deposited 2010-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–111（94 aa）
Fragment：p53 binding domain
|
Mutation：L33E | K23 6-chloro-3-[1-(4-chlorobenzyl)-4-phenyl-1H-imidazol-5-yl]-1H-indole-2-carboxylic acid × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；300 K；0.1M sodium-acetate-trihydrate, 2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 2.30 Å R-free 0.251 |
| 3LBK Structure of human MDM2 protein in complex with a small molecule inhibitor Deposited 2010-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
18–111（94 aa）
Fragment：p53 binding domain
|
Mutation：L33E | K23 6-chloro-3-[1-(4-chlorobenzyl)-4-phenyl-1H-imidazol-5-yl]-1H-indole-2-carboxylic acid × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；300 K；0.1M sodium-acetate-trihydrate, 2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 2.30 Å R-free 0.251 |
| 3LBL Structure of human MDM2 protein in complex with Mi-63-analog Deposited 2010-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–111（94 aa）
Fragment：p53 binding domain
|
Not recorded | MI6 (2'R,3R,4'R,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(2-morpholin-4-ylethyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；300 K；0.1M sodium-acetate-trihydrate, 2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 1.60 Å R-free 0.236 |
| 3LBL Structure of human MDM2 protein in complex with Mi-63-analog Deposited 2010-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
18–111（94 aa）
Fragment：p53 binding domain
|
Not recorded | MI6 (2'R,3R,4'R,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(2-morpholin-4-ylethyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；300 K；0.1M sodium-acetate-trihydrate, 2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 1.60 Å R-free 0.236 |
| 3LBL Structure of human MDM2 protein in complex with Mi-63-analog Deposited 2010-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
18–111（94 aa）
Fragment：p53 binding domain
|
Not recorded | MI6 (2'R,3R,4'R,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(2-morpholin-4-ylethyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；300 K；0.1M sodium-acetate-trihydrate, 2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 1.60 Å R-free 0.236 |
| 3LNJ Crystal structure of human MDM2 in complex with D-peptide inhibitor (DPMI-alpha) Deposited 2010-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
25–109（85 aa）
Fragment：UNP residues 25-109, P53 BINDING DOMAIN
Chain C
25–109（85 aa）
Fragment：UNP residues 25-109, P53 BINDING DOMAIN
|
Not recorded | SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；273 K；0.2 M
ammonium sulfate, 0.1 M sodium cacodylate trihydrate, and 30%
PEG 8000, pH 6.5., VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 2.40 Å R-free 0.255 |
| 3LNJ Crystal structure of human MDM2 in complex with D-peptide inhibitor (DPMI-alpha) Deposited 2010-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
25–109（85 aa）
Fragment：UNP residues 25-109, P53 BINDING DOMAIN
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；273 K；0.2 M
ammonium sulfate, 0.1 M sodium cacodylate trihydrate, and 30%
PEG 8000, pH 6.5., VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 2.40 Å R-free 0.255 |
| 3LNZ Crystal structure of human MDM2 with a 12-mer peptide inhibitor PMI (N8A mutant) Deposited 2010-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
25–109（85 aa）
Fragment：UNP residues 25-109, P53 BINDING DOMAIN
|
Not recorded | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；273 K；0.2 M Mg acetate tetrahydrate sulfate, 0.1 M cacodylate trihydrate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 1.95 Å R-free 0.267 |
| 3LNZ Crystal structure of human MDM2 with a 12-mer peptide inhibitor PMI (N8A mutant) Deposited 2010-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
25–109（85 aa）
Fragment：UNP residues 25-109, P53 BINDING DOMAIN
|
Not recorded | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；273 K；0.2 M Mg acetate tetrahydrate sulfate, 0.1 M cacodylate trihydrate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 1.95 Å R-free 0.267 |
| 3LNZ Crystal structure of human MDM2 with a 12-mer peptide inhibitor PMI (N8A mutant) Deposited 2010-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
25–109（85 aa）
Fragment：UNP residues 25-109, P53 BINDING DOMAIN
Chain G
25–109（85 aa）
Fragment：UNP residues 25-109, P53 BINDING DOMAIN
|
Not recorded | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；273 K；0.2 M Mg acetate tetrahydrate sulfate, 0.1 M cacodylate trihydrate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 1.95 Å R-free 0.267 |
| 3LNZ Crystal structure of human MDM2 with a 12-mer peptide inhibitor PMI (N8A mutant) Deposited 2010-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain I
25–109（85 aa）
Fragment：UNP residues 25-109, P53 BINDING DOMAIN
Chain K
25–109（85 aa）
Fragment：UNP residues 25-109, P53 BINDING DOMAIN
|
Not recorded | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；273 K；0.2 M Mg acetate tetrahydrate sulfate, 0.1 M cacodylate trihydrate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 1.95 Å R-free 0.267 |
| 3LNZ Crystal structure of human MDM2 with a 12-mer peptide inhibitor PMI (N8A mutant) Deposited 2010-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain M
25–109（85 aa）
Fragment：UNP residues 25-109, P53 BINDING DOMAIN
|
Not recorded | CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；273 K；0.2 M Mg acetate tetrahydrate sulfate, 0.1 M cacodylate trihydrate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 1.95 Å R-free 0.267 |
| 3LNZ Crystal structure of human MDM2 with a 12-mer peptide inhibitor PMI (N8A mutant) Deposited 2010-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain O
25–109（85 aa）
Fragment：UNP residues 25-109, P53 BINDING DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；273 K；0.2 M Mg acetate tetrahydrate sulfate, 0.1 M cacodylate trihydrate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
|
Resolution 1.95 Å R-free 0.267 |
| 3TJ2 Structure of a novel submicromolar MDM2 inhibitor Deposited 2011-08-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–111（94 aa）
Fragment：p53 binding domain (UNP Residues 18-111)
|
Not recorded | TJ2 3-{(1S)-2-(tert-butylamino)-1-[(4-chlorobenzyl)(formyl)amino]-2-oxoethyl}-6-chloro-1H-indole-2-carboxylic acid × 1 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277.15 K；0.15 M Potassium bromide, 30% Polyethylene glycol mono methyl ether 2000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
|
Resolution 2.10 Å R-free 0.308 |
| 3TJ2 Structure of a novel submicromolar MDM2 inhibitor Deposited 2011-08-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
18–111（94 aa）
Fragment：p53 binding domain (UNP Residues 18-111)
|
Not recorded | TJ2 3-{(1S)-2-(tert-butylamino)-1-[(4-chlorobenzyl)(formyl)amino]-2-oxoethyl}-6-chloro-1H-indole-2-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277.15 K；0.15 M Potassium bromide, 30% Polyethylene glycol mono methyl ether 2000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
|
Resolution 2.10 Å R-free 0.308 |
| 3TPX Crystal structure of human MDM2 in complex with a trifluoromethylated D-peptide inhibitor Deposited 2011-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
25–109（85 aa）
Fragment：p53 binding domain (UNP residues 25-109)
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M MES, pH 5.5, 25% PEG4000, 0.15 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.231 |
| 3TPX Crystal structure of human MDM2 in complex with a trifluoromethylated D-peptide inhibitor Deposited 2011-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
25–109（85 aa）
Fragment：p53 binding domain (UNP residues 25-109)
|
Not recorded | SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M MES, pH 5.5, 25% PEG4000, 0.15 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.231 |
| 3TPX Crystal structure of human MDM2 in complex with a trifluoromethylated D-peptide inhibitor Deposited 2011-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
25–109（85 aa）
Fragment：p53 binding domain (UNP residues 25-109)
|
Not recorded | CL CHLORIDE ION × 3 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M MES, pH 5.5, 25% PEG4000, 0.15 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.231 |
| 3TU1 Exhaustive Fluorine Scanning towards Potent p53-MDM2 Antagonist Deposited 2011-09-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–125（108 aa）
Fragment：p53 binding domain (UNP Residues 18-105)
|
Not recorded | 07G 3-[(1S)-2-(tert-butylamino)-1-{N-[(3,4-difluorophenyl)methyl]formamido}-2-oxoethyl]-6-chloro-1H-indole-2-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.8；277 K；0.1 M sodium acetate
18% PEG 4000
, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.60 Å R-free 0.245 |
| 3V3B Structure of the Stapled p53 Peptide Bound to Mdm2 Deposited 2011-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
24–110（87 aa）
|
Not recorded | CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.75；290 K；100 mM Na-acetate, 2.5M NaCl, pH 4.75, VAPOR DIFFUSION, SITTING DROP, temperature 290K
|
Resolution 2.00 Å R-free 0.216 |
| 3V3B Structure of the Stapled p53 Peptide Bound to Mdm2 Deposited 2011-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
24–110（87 aa）
|
Not recorded | CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.75；290 K；100 mM Na-acetate, 2.5M NaCl, pH 4.75, VAPOR DIFFUSION, SITTING DROP, temperature 290K
|
Resolution 2.00 Å R-free 0.216 |
| 3V3B Structure of the Stapled p53 Peptide Bound to Mdm2 Deposited 2011-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
24–110（87 aa）
Chain B
24–110（87 aa）
|
Not recorded | CL CHLORIDE ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.75；290 K；100 mM Na-acetate, 2.5M NaCl, pH 4.75, VAPOR DIFFUSION, SITTING DROP, temperature 290K
|
Resolution 2.00 Å R-free 0.216 |
| 3VBG Structure of hDM2 with Dimer Inducing Indolyl Hydantoin RO-2443 Deposited 2012-01-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
25–109（85 aa）
Fragment：unp residues 25-109
Chain B
25–109（85 aa）
Fragment：unp residues 25-109
|
Not recorded | 03M (5Z)-5-[(6-chloro-7-methyl-1H-indol-3-yl)methylidene]-3-(3,4-difluorobenzyl)imidazolidine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；54% saturated ammonium sulfate, 0.1M Tris, 5% PEG 550 mme, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.5
|
Resolution 2.80 Å R-free 0.220 |
| 3VBG Structure of hDM2 with Dimer Inducing Indolyl Hydantoin RO-2443 Deposited 2012-01-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
25–109（85 aa）
Fragment：unp residues 25-109
Chain D
25–109（85 aa）
Fragment：unp residues 25-109
|
Not recorded | 03M (5Z)-5-[(6-chloro-7-methyl-1H-indol-3-yl)methylidene]-3-(3,4-difluorobenzyl)imidazolidine-2,4-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；54% saturated ammonium sulfate, 0.1M Tris, 5% PEG 550 mme, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.5
|
Resolution 2.80 Å R-free 0.220 |
| 3VZV Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor Deposited 2012-10-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
25–109（85 aa）
Fragment：SWIB domain, UNP residues 25-109
|
Mutation：L33E | VZV 1-{[(5R,6S)-5,6-bis(4-chlorophenyl)-6-methyl-3-(propan-2-yl)-5,6-dihydroimidazo[2,1-b][1,3]thiazol-2-yl]carbonyl}-N,N-dimethyl-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；2.4M Ammonium sulfate, 5% PEG 200, 0.1M Tris HCl, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.284 |
| 3VZV Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor Deposited 2012-10-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
25–109（85 aa）
Fragment：SWIB domain, UNP residues 25-109
|
Mutation：L33E | VZV 1-{[(5R,6S)-5,6-bis(4-chlorophenyl)-6-methyl-3-(propan-2-yl)-5,6-dihydroimidazo[2,1-b][1,3]thiazol-2-yl]carbonyl}-N,N-dimethyl-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；2.4M Ammonium sulfate, 5% PEG 200, 0.1M Tris HCl, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.284 |
| 3W69 Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor Deposited 2013-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
25–109（85 aa）
Fragment：UNP residues 25-109
|
Mutation：L33E | LTZ (5R,6S)-2-[((2S,5R)-2-{[(3R)-4-acetyl-3-methylpiperazin-1-yl]carbonyl}-5-ethylpyrrolidin-1-yl)carbonyl]-5,6-bis(4-chlorophenyl)-3-isopropyl-6-methyl-5,6-dihydroimidazo[2,1-b][1,3]thiazole × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；2.4M Ammonium sulfate, 5% PEG 200, 0.1M Tris HCl, pH 8.1 , VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.238 |
| 3W69 Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor Deposited 2013-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
25–109（85 aa）
Fragment：UNP residues 25-109
|
Mutation：L33E | LTZ (5R,6S)-2-[((2S,5R)-2-{[(3R)-4-acetyl-3-methylpiperazin-1-yl]carbonyl}-5-ethylpyrrolidin-1-yl)carbonyl]-5,6-bis(4-chlorophenyl)-3-isopropyl-6-methyl-5,6-dihydroimidazo[2,1-b][1,3]thiazole × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；2.4M Ammonium sulfate, 5% PEG 200, 0.1M Tris HCl, pH 8.1 , VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.238 |
| 4DIJ The Central Valine Concept Provides an Entry in a New Class of Non Peptide Inhibitors of the P53-MDM2 Interaction Deposited 2012-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：N-TERMINAL DOMAIN, P53-BINDING DOMAIN, UNP RESIDUES 17-111
|
Mutation：L33E | BLF 6-chloro-3-[1-(4-chlorobenzyl)-4-phenyl-1H-imidazol-5-yl]-N-[2-(morpholin-4-yl)ethyl]-1H-indole-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1M Tris, 0.2M LiSO4, 22% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.224 |
| 4DIJ The Central Valine Concept Provides an Entry in a New Class of Non Peptide Inhibitors of the P53-MDM2 Interaction Deposited 2012-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–111（95 aa）
Fragment：N-TERMINAL DOMAIN, P53-BINDING DOMAIN, UNP RESIDUES 17-111
|
Mutation：L33E | BLF 6-chloro-3-[1-(4-chlorobenzyl)-4-phenyl-1H-imidazol-5-yl]-N-[2-(morpholin-4-yl)ethyl]-1H-indole-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1M Tris, 0.2M LiSO4, 22% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.224 |
| 4ERE crystal structure of MDM2 (17-111) in complex with compound 23 Deposited 2012-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：unp residues 17-111
|
Not recorded | 0R2 [(3R,5R,6S)-1-[(2S)-1-tert-butoxy-1-oxobutan-2-yl]-5-(3-chlorophenyl)-6-(4-chlorophenyl)-2-oxopiperidin-3-yl]acetic acid × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；100 mM MES, 2.7-3.2 M Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.270 |
| 4ERE crystal structure of MDM2 (17-111) in complex with compound 23 Deposited 2012-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–111（95 aa）
Fragment：unp residues 17-111
|
Not recorded | 0R2 [(3R,5R,6S)-1-[(2S)-1-tert-butoxy-1-oxobutan-2-yl]-5-(3-chlorophenyl)-6-(4-chlorophenyl)-2-oxopiperidin-3-yl]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；100 mM MES, 2.7-3.2 M Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.270 |
| 4ERF crystal structure of MDM2 (17-111) in complex with compound 29 (AM-8553) Deposited 2012-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：unp residues 17-111
|
Not recorded | 0R3 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S,3S)-2-hydroxypentan-3-yl]-3-methyl-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, 1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.00 Å R-free 0.250 |
| 4ERF crystal structure of MDM2 (17-111) in complex with compound 29 (AM-8553) Deposited 2012-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
17–111（95 aa）
Fragment：unp residues 17-111
|
Not recorded | 0R3 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S,3S)-2-hydroxypentan-3-yl]-3-methyl-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, 1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.00 Å R-free 0.250 |
| 4ERF crystal structure of MDM2 (17-111) in complex with compound 29 (AM-8553) Deposited 2012-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
17–111（95 aa）
Fragment：unp residues 17-111
|
Not recorded | 0R3 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S,3S)-2-hydroxypentan-3-yl]-3-methyl-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, 1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.00 Å R-free 0.250 |
| 4HBM Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors Deposited 2012-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
6–125（120 aa）
|
Not recorded | 0Y7 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, pH 5.0
1.5-2.0 M (NH4)2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.240 |
| 4HBM Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors Deposited 2012-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 10 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
6–125（120 aa）
Chain E
6–125（120 aa）
|
Not recorded | 0Y7 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, pH 5.0
1.5-2.0 M (NH4)2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.240 |
| 4HBM Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors Deposited 2012-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 11 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain D
6–125（120 aa）
Chain F
6–125（120 aa）
|
Not recorded | 0Y7 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, pH 5.0
1.5-2.0 M (NH4)2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.240 |
| 4HBM Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors Deposited 2012-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 12 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain G
6–125（120 aa）
Chain H
6–125（120 aa）
|
Not recorded | 0Y7 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, pH 5.0
1.5-2.0 M (NH4)2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.240 |
| 4HBM Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors Deposited 2012-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
6–125（120 aa）
|
Not recorded | 0Y7 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, pH 5.0
1.5-2.0 M (NH4)2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.240 |
| 4HBM Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors Deposited 2012-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
6–125（120 aa）
|
Not recorded | 0Y7 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, pH 5.0
1.5-2.0 M (NH4)2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.240 |
| 4HBM Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors Deposited 2012-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
6–125（120 aa）
|
Not recorded | 0Y7 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, pH 5.0
1.5-2.0 M (NH4)2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.240 |
| 4HBM Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors Deposited 2012-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
6–125（120 aa）
|
Not recorded | 0Y7 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, pH 5.0
1.5-2.0 M (NH4)2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.240 |
| 4HBM Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors Deposited 2012-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
6–125（120 aa）
|
Not recorded | 0Y7 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, pH 5.0
1.5-2.0 M (NH4)2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.240 |
| 4HBM Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors Deposited 2012-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain G
6–125（120 aa）
|
Not recorded | 0Y7 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, pH 5.0
1.5-2.0 M (NH4)2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.240 |
| 4HBM Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors Deposited 2012-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain H
6–125（120 aa）
|
Not recorded | 0Y7 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, pH 5.0
1.5-2.0 M (NH4)2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.240 |
| 4HBM Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors Deposited 2012-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 9 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
6–125（120 aa）
Chain B
6–125（120 aa）
|
Not recorded | 0Y7 {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, pH 5.0
1.5-2.0 M (NH4)2SO4 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.240 |
| 4HFZ Crystal Structure of an MDM2/P53 Peptide Complex Deposited 2012-10-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–125（109 aa）
Fragment：p53 binding domain (residues 17-125)
|
Mutation：E69A, K70A | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.2 M (NH4)2SO4, pH 4.6 and 30% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.69 Å R-free 0.247 |
| 4HFZ Crystal Structure of an MDM2/P53 Peptide Complex Deposited 2012-10-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
17–125（109 aa）
Fragment：p53 binding domain (residues 17-125)
|
Mutation：E69A, K70A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.2 M (NH4)2SO4, pH 4.6 and 30% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.69 Å R-free 0.247 |
| 4HG7 Crystal Structure of an MDM2/Nutlin-3a complex Deposited 2012-10-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–108（92 aa）
Fragment：p53 binding domain (residues 17-125)
|
Mutation：E69A, K70A | NUT 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.5 M ammonium sulfate, 0.1 M sodium citrate, 1.0 M lithium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.60 Å R-free 0.215 |
| 4HG7 Crystal Structure of an MDM2/Nutlin-3a complex Deposited 2012-10-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
17–108（92 aa）
Fragment：p53 binding domain (residues 17-125)
|
Mutation：E69A, K70A | NUT 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.5 M ammonium sulfate, 0.1 M sodium citrate, 1.0 M lithium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.60 Å R-free 0.215 |
| 4JV7 Co-crystal structure of MDM2 with inhibitor (2S,5R,6S)-2-benzyl-5,6-bis(4-bromophenyl)-4-methylmorpholin-3-one Deposited 2013-03-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–111（94 aa）
Fragment：UNP residues 18-111
|
Not recorded | 1MN (2S,5R,6S)-2-benzyl-5,6-bis(4-bromophenyl)-4-methylmorpholin-3-one × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；100 mM HEPES, pH 7.0, 2.1-2.6 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.281 |
| 4JV9 Co-crystal structure of MDM2 with inhibitor (2S,5R,6S)-2-benzyl-5,6-bis(4-chlorophenyl)-4-methylmorpholin-3-one Deposited 2013-03-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–111（94 aa）
Fragment：UNP residues 18-111
|
Not recorded | 1MO (2S,5R,6S)-2-benzyl-5,6-bis(4-chlorophenyl)-4-methylmorpholin-3-one × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；100 mM HEPES, pH 7.0, 2.1-2.6 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.50 Å R-free 0.270 |
| 4JVE Co-crystal structure of MDM2 with inhibitor (2R,3E)-2-[(2S,3R,6S)-2,3-bis(4-chlorophenyl)-6-(4-fluorobenzyl)-5-oxomorpholin-4-yl]pent-3-enoic acid Deposited 2013-03-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–111（94 aa）
Fragment：UNP residues 18-111
|
Not recorded | 1MQ (2R,3E)-2-[(2S,3R,6S)-2,3-bis(4-chlorophenyl)-6-(4-fluorobenzyl)-5-oxomorpholin-4-yl]pent-3-enoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；277 K；100 mM Bicine, pH 9.0, 1.6 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.298 |
| 4JVR Co-crystal structure of MDM2 with inhibitor (2'S,3R,4'S,5'R)-N-(2-aminoethyl)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide Deposited 2013-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–111（94 aa）
Fragment：UNP residues 18-111
|
Not recorded | 1MT (2'S,3R,4'S,5'R)-N-(2-aminoethyl)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM citrate, pH 5.0, 1.5-2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.270 |
| 4JVR Co-crystal structure of MDM2 with inhibitor (2'S,3R,4'S,5'R)-N-(2-aminoethyl)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide Deposited 2013-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
18–111（94 aa）
Fragment：UNP residues 18-111
|
Not recorded | 1MT (2'S,3R,4'S,5'R)-N-(2-aminoethyl)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM citrate, pH 5.0, 1.5-2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.270 |
| 4JVR Co-crystal structure of MDM2 with inhibitor (2'S,3R,4'S,5'R)-N-(2-aminoethyl)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide Deposited 2013-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
18–111（94 aa）
Fragment：UNP residues 18-111
|
Not recorded | 1MT (2'S,3R,4'S,5'R)-N-(2-aminoethyl)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM citrate, pH 5.0, 1.5-2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.270 |
| 4JWR Co-crystal structure of MDM2 with inhibitor {(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3-oxomorpholin-2-yl}acetic acid Deposited 2013-03-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：UNP residues 17-111
|
Not recorded | 1MY {(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3-oxomorpholin-2-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM citrate, pH 5.0, 1.9-2.4 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.35 Å R-free 0.266 |
| 4JWR Co-crystal structure of MDM2 with inhibitor {(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3-oxomorpholin-2-yl}acetic acid Deposited 2013-03-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–111（95 aa）
Fragment：UNP residues 17-111
|
Not recorded | 1MY {(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3-oxomorpholin-2-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM citrate, pH 5.0, 1.9-2.4 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.35 Å R-free 0.266 |
| 4JWR Co-crystal structure of MDM2 with inhibitor {(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3-oxomorpholin-2-yl}acetic acid Deposited 2013-03-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
17–111（95 aa）
Fragment：UNP residues 17-111
|
Not recorded | 1MY {(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3-oxomorpholin-2-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM citrate, pH 5.0, 1.9-2.4 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.35 Å R-free 0.266 |
| 4MDN Structure of a novel submicromolar MDM2 inhibitor Deposited 2013-08-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–110（93 aa）
Fragment：UNP residues 18-110
|
Not recorded | Y30 3-{(1S)-2-(tert-butylamino)-1-[{4-[(4-chlorobenzyl)oxy]benzyl}(formyl)amino]-2-oxoethyl}-6-chloro-1H-indole-2-carboxylic acid × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M ammonium nitrate, 20% w/v PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.91 Å R-free 0.203 |
| 4MDQ Structure of a novel submicromolar MDM2 inhibitor Deposited 2013-08-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
25–110（86 aa）
Fragment：UNP residues 25-110
|
Not recorded | 28W 3-[(1R)-2-(benzylamino)-1-{[(2S)-1-(hydroxyamino)-4-methyl-1-oxopentan-2-yl]amino}-2-oxoethyl]-6-chloro-N-hydroxy-1H-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M ammonium nitrate, 20% w/v PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.12 Å R-free 0.221 |
| 4OAS co-crystal structure of MDM2 (17-111) in complex with compound 25 Deposited 2014-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：UNP Residues 17-111
|
Not recorded | 2SW [(3R,5R,6S)-1-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-5-(3-chlorophenyl)-6-(4-chlorophenyl)-3-methyl-2-oxopiperidin-3-yl]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, 1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.239 |
| 4OAS co-crystal structure of MDM2 (17-111) in complex with compound 25 Deposited 2014-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
17–111（95 aa）
Fragment：UNP Residues 17-111
|
Not recorded | 2SW [(3R,5R,6S)-1-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-5-(3-chlorophenyl)-6-(4-chlorophenyl)-3-methyl-2-oxopiperidin-3-yl]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, 1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.239 |
| 4OAS co-crystal structure of MDM2 (17-111) in complex with compound 25 Deposited 2014-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
17–111（95 aa）
Fragment：UNP Residues 17-111
|
Not recorded | 2SW [(3R,5R,6S)-1-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-5-(3-chlorophenyl)-6-(4-chlorophenyl)-3-methyl-2-oxopiperidin-3-yl]acetic acid × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, 1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.239 |
| 4OBA Co-crystal structure of MDM2 with Inhibitor Compound 4 Deposited 2014-01-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：UNP Residues 17-111
|
Not recorded | 2TW [(2R,5R,6R)-4-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；1.6-2.3M Ammonium Sulfate, 0.1M citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.60 Å R-free 0.313 |
| 4OBA Co-crystal structure of MDM2 with Inhibitor Compound 4 Deposited 2014-01-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–111（95 aa）
Fragment：UNP Residues 17-111
|
Not recorded | 2TW [(2R,5R,6R)-4-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；1.6-2.3M Ammonium Sulfate, 0.1M citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.60 Å R-free 0.313 |
| 4OBA Co-crystal structure of MDM2 with Inhibitor Compound 4 Deposited 2014-01-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
17–111（95 aa）
Fragment：UNP Residues 17-111
|
Not recorded | 2TW [(2R,5R,6R)-4-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；1.6-2.3M Ammonium Sulfate, 0.1M citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.60 Å R-free 0.313 |
| 4OCC co-crystal structure of MDM2(17-111) in complex with compound 48 Deposited 2014-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
|
Not recorded | 2TZ [(2R,5R,6R)-4-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, 1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.216 |
| 4OCC co-crystal structure of MDM2(17-111) in complex with compound 48 Deposited 2014-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
17–111（95 aa）
|
Not recorded | 2TZ [(2R,5R,6R)-4-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, 1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.216 |
| 4OCC co-crystal structure of MDM2(17-111) in complex with compound 48 Deposited 2014-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
17–111（95 aa）
|
Not recorded | 2TZ [(2R,5R,6R)-4-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate, 1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.216 |
| 4ODE Co-Crystal Structure of MDM2 with Inhibitor Compound 4 Deposited 2014-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
6–110（105 aa）
Fragment：UNP Residues 6-110
|
Not recorded | 2U0 (2-{[(3R,5R,6S)-1-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(4-chloro-3-fluorophenyl)-5-(3-chlorophenyl)-3-methyl-2-oxopiperidin-3-yl]methyl}-1,3-thiazol-5-yl)acetic acid × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.8-1.8M Ammonium Sulfate, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.216 |
| 4ODF Co-Crystal Structure of MDM2 with Inhibitor Compound 47 Deposited 2014-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
6–110（105 aa）
Fragment：UNP Residues 6-110
|
Not recorded | 2U1 6-{[(2S,5R,6R)-4-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-2-methyl-3-oxomorpholin-2-yl]methyl}pyridine-3-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.8-1.8M Ammonium Sulfate, 0.1M sodium Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.305 |
| 4OGN Co-Crystal Structure of MDM2 with Inhbitor Compound 3 Deposited 2014-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
6–110（105 aa）
Fragment：UNP Residues 6-110
|
Not recorded | 2U5 6-{[(3R,5R,6S)-1-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-5-(3-chlorophenyl)-6-(4-chlorophenyl)-3-methyl-2-oxopiperidin-3-yl]methyl}pyridine-3-carboxylic acid × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.8-1.8M Ammonium Sulfate, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.38 Å R-free 0.223 |
| 4OGT Co-Crystal Structure of MDM2 with Inhbitor Compound 46 Deposited 2014-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
6–110（105 aa）
Fragment：UNP Residue 6-110
|
Not recorded | 2U6 6-{[(2R,5R,6R)-4-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-2-methyl-3-oxomorpholin-2-yl]methyl}pyridine-3-carboxylic acid × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.8-1.8M Ammonium Sulfate, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.54 Å R-free 0.225 |
| 4OGV Co-Crystal Structure of MDM2 with Inhibitor Compound 49 Deposited 2014-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：UNP Residues 7-111
|
Not recorded | 2U7 [(2S,5R,6R)-4-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；1.6-2.3M Ammonium Sulfate, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.283 |
| 4OGV Co-Crystal Structure of MDM2 with Inhibitor Compound 49 Deposited 2014-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–111（95 aa）
Fragment：UNP Residues 7-111
|
Not recorded | 2U7 [(2S,5R,6R)-4-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；1.6-2.3M Ammonium Sulfate, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.283 |
| 4OGV Co-Crystal Structure of MDM2 with Inhibitor Compound 49 Deposited 2014-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
17–111（95 aa）
Fragment：UNP Residues 7-111
|
Not recorded | 2U7 [(2S,5R,6R)-4-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；1.6-2.3M Ammonium Sulfate, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.283 |
| 4OQ3 Tetra-substituted imidazoles as a new class of inhibitors of the p53-MDM2 interaction Deposited 2014-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：N-TERMINAL DOMAIN, UNP residues 17-111
|
Mutation：L33E | 2V8 1-(5-chloro-2-methylphenyl)-5-(3-chlorophenyl)-2-(3-methylphenyl)-1H-imidazole-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；2.4M AmSO4, 0.1M Tris, 0.1M NaCitrate, pH 8.0, vapor diffusion, hanging drop, temperature 298K
|
Resolution 2.30 Å R-free 0.224 |
| 4OQ3 Tetra-substituted imidazoles as a new class of inhibitors of the p53-MDM2 interaction Deposited 2014-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–111（95 aa）
Fragment：N-TERMINAL DOMAIN, UNP residues 17-111
|
Mutation：L33E | 2V8 1-(5-chloro-2-methylphenyl)-5-(3-chlorophenyl)-2-(3-methylphenyl)-1H-imidazole-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；2.4M AmSO4, 0.1M Tris, 0.1M NaCitrate, pH 8.0, vapor diffusion, hanging drop, temperature 298K
|
Resolution 2.30 Å R-free 0.224 |
| 4OQ3 Tetra-substituted imidazoles as a new class of inhibitors of the p53-MDM2 interaction Deposited 2014-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
17–111（95 aa）
Fragment：N-TERMINAL DOMAIN, UNP residues 17-111
|
Mutation：L33E | 2V8 1-(5-chloro-2-methylphenyl)-5-(3-chlorophenyl)-2-(3-methylphenyl)-1H-imidazole-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；2.4M AmSO4, 0.1M Tris, 0.1M NaCitrate, pH 8.0, vapor diffusion, hanging drop, temperature 298K
|
Resolution 2.30 Å R-free 0.224 |
| 4OQ3 Tetra-substituted imidazoles as a new class of inhibitors of the p53-MDM2 interaction Deposited 2014-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
17–111（95 aa）
Fragment：N-TERMINAL DOMAIN, UNP residues 17-111
|
Mutation：L33E | 2V8 1-(5-chloro-2-methylphenyl)-5-(3-chlorophenyl)-2-(3-methylphenyl)-1H-imidazole-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；2.4M AmSO4, 0.1M Tris, 0.1M NaCitrate, pH 8.0, vapor diffusion, hanging drop, temperature 298K
|
Resolution 2.30 Å R-free 0.224 |
| 4QO4 co-crystal structure of MDM2 (17-111) with compound 16, {(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-(6-CYCLOPROPYLPYRIDIN-2-YL)PROPYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID Deposited 2014-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
|
Not recorded | 35S {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(1S)-1-(6-cyclopropylpyridin-2-yl)propyl]-3-methyl-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate,
1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.302 |
| 4QOC crystal structure of compound 16 bound to MDM2(17-111), {(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID Deposited 2014-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
|
Not recorded | 35T {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(1S)-1-cyclopropyl-2-(pyrrolidin-1-ylsulfonyl)ethyl]-3-methyl-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate,
1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.253 |
| 4QOC crystal structure of compound 16 bound to MDM2(17-111), {(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID Deposited 2014-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
17–111（95 aa）
|
Not recorded | 35T {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(1S)-1-cyclopropyl-2-(pyrrolidin-1-ylsulfonyl)ethyl]-3-methyl-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate,
1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.253 |
| 4QOC crystal structure of compound 16 bound to MDM2(17-111), {(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID Deposited 2014-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
17–111（95 aa）
|
Not recorded | 35T {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(1S)-1-cyclopropyl-2-(pyrrolidin-1-ylsulfonyl)ethyl]-3-methyl-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate,
1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.253 |
| 4QOC crystal structure of compound 16 bound to MDM2(17-111), {(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID Deposited 2014-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain G
17–111（95 aa）
|
Not recorded | 35T {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(1S)-1-cyclopropyl-2-(pyrrolidin-1-ylsulfonyl)ethyl]-3-methyl-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate,
1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.253 |
| 4QOC crystal structure of compound 16 bound to MDM2(17-111), {(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID Deposited 2014-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain I
17–111（95 aa）
|
Not recorded | 35T {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(1S)-1-cyclopropyl-2-(pyrrolidin-1-ylsulfonyl)ethyl]-3-methyl-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate,
1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.253 |
| 4QOC crystal structure of compound 16 bound to MDM2(17-111), {(3R,5R,6S)-5-(3-CHLOROPHENYL)-6-(4-CHLOROPHENYL)-1-[(1S)-1-CYCLOPROPYL-2-(PYRROLIDIN-1-YLSULFONYL)ETHYL]-3-METHYL-2-OXOPIPERIDIN-3-YL}ACETIC ACID Deposited 2014-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain K
17–111（95 aa）
|
Not recorded | 35T {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(1S)-1-cyclopropyl-2-(pyrrolidin-1-ylsulfonyl)ethyl]-3-methyl-2-oxopiperidin-3-yl}acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100 mM Citrate,
1.9-2.4 M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.70 Å R-free 0.253 |
| 4UD7 Structure of the stapled peptide YS-02 bound to MDM2 Deposited 2014-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
17–125（109 aa）
Fragment：P53 BINDING DOMAIN, UNP RESIDUES 17-125
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4；0.1 M SODIUM CITRATE PH 4.0 AND 15 % PEG8000
|
Resolution 1.60 Å R-free 0.178 |
| 4UD7 Structure of the stapled peptide YS-02 bound to MDM2 Deposited 2014-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
17–125（109 aa）
Fragment：P53 BINDING DOMAIN, UNP RESIDUES 17-125
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4；0.1 M SODIUM CITRATE PH 4.0 AND 15 % PEG8000
|
Resolution 1.60 Å R-free 0.178 |
| 4UD7 Structure of the stapled peptide YS-02 bound to MDM2 Deposited 2014-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
17–125（109 aa）
Fragment：P53 BINDING DOMAIN, UNP RESIDUES 17-125
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4；0.1 M SODIUM CITRATE PH 4.0 AND 15 % PEG8000
|
Resolution 1.60 Å R-free 0.178 |
| 4UD7 Structure of the stapled peptide YS-02 bound to MDM2 Deposited 2014-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–125（109 aa）
Fragment：P53 BINDING DOMAIN, UNP RESIDUES 17-125
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4；0.1 M SODIUM CITRATE PH 4.0 AND 15 % PEG8000
|
Resolution 1.60 Å R-free 0.178 |
| 4UE1 Structure of the stapled peptide YS-01 bound to MDM2 Deposited 2014-12-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
17–125（109 aa）
Fragment：P53 BINDING DOMAIN, RESIDUES 17-125
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.2；0.1 M SODIUM CITRATE PH 4.2, 0.2 M SODIUM CHLORIDE AND 20 % PEG8000
|
Resolution 1.45 Å R-free 0.184 |
| 4UE1 Structure of the stapled peptide YS-01 bound to MDM2 Deposited 2014-12-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
17–125（109 aa）
Fragment：P53 BINDING DOMAIN, RESIDUES 17-125
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.2；0.1 M SODIUM CITRATE PH 4.2, 0.2 M SODIUM CHLORIDE AND 20 % PEG8000
|
Resolution 1.45 Å R-free 0.184 |
| 4UE1 Structure of the stapled peptide YS-01 bound to MDM2 Deposited 2014-12-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–125（109 aa）
Fragment：P53 BINDING DOMAIN, RESIDUES 17-125
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.2；0.1 M SODIUM CITRATE PH 4.2, 0.2 M SODIUM CHLORIDE AND 20 % PEG8000
|
Resolution 1.45 Å R-free 0.184 |
| 4UE1 Structure of the stapled peptide YS-01 bound to MDM2 Deposited 2014-12-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
17–125（109 aa）
Fragment：P53 BINDING DOMAIN, RESIDUES 17-125
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.2；0.1 M SODIUM CITRATE PH 4.2, 0.2 M SODIUM CHLORIDE AND 20 % PEG8000
|
Resolution 1.45 Å R-free 0.184 |
| 4UMN Structure of a stapled peptide antagonist bound to Nutlin-resistant Mdm2. Deposited 2014-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
6–125（120 aa）
Fragment：P53 BINDING DOMAIN, RESIDUES 6-125
Chain B
6–125（120 aa）
Fragment：P53 BINDING DOMAIN, RESIDUES 6-125
|
Mutation：YES Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.4；289 K；0.04 M CITRIC ACID, 0.06 M BIS-TRIS PROPANE PH 6.4, AND 20% PEG 3350
|
Resolution 1.99 Å R-free 0.237 |
| 4WT2 Co-crystal Structure of MDM2 in Complex with AM-7209 Deposited 2014-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
12–116（105 aa）
Fragment：UNP RESIDUES 12-116
|
Not recorded | 3UD 4-({[(3R,5R,6S)-1-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(4-chloro-3-fluorophenyl)-5-(3-chlorophenyl)-3-methyl-2-oxopiperidin-3-yl]acetyl}amino)-2-methoxybenzoic acid × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；1.4M Ammonium Sulfate, 0.1M Sodium Citrate
|
Resolution 1.42 Å R-free 0.192 |
| 4XXB Crystal structure of human MDM2-RPL11 Deposited 2015-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
290–437（148 aa）
Fragment：UNP residues 293-334
|
Not recorded | IMD IMIDAZOLE × 1 BME BETA-MERCAPTOETHANOL × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；peg
|
Resolution 2.40 Å R-free 0.227 |
| 4ZFI Structure of Mdm2 with low molecular weight inhibitor Deposited 2015-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
24–119（96 aa）
Fragment：UNP RESIDUES 18-113
|
Not recorded | 4NJ (5S)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxy-1-methyl-1,5-dihydro-2H-pyrrol-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5, 0.2 M sodium chloride, 25% (w/v) PEG 3350
|
Resolution 2.00 Å R-free 0.243 |
| 4ZFI Structure of Mdm2 with low molecular weight inhibitor Deposited 2015-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
24–119（96 aa）
Fragment：UNP RESIDUES 18-113
|
Not recorded | 4NJ (5S)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxy-1-methyl-1,5-dihydro-2H-pyrrol-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5, 0.2 M sodium chloride, 25% (w/v) PEG 3350
|
Resolution 2.00 Å R-free 0.243 |
| 4ZFI Structure of Mdm2 with low molecular weight inhibitor Deposited 2015-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
24–119（96 aa）
Fragment：UNP RESIDUES 18-113
|
Not recorded | 4NJ (5S)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxy-1-methyl-1,5-dihydro-2H-pyrrol-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5, 0.2 M sodium chloride, 25% (w/v) PEG 3350
|
Resolution 2.00 Å R-free 0.243 |
| 4ZFI Structure of Mdm2 with low molecular weight inhibitor Deposited 2015-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
24–119（96 aa）
Fragment：UNP RESIDUES 18-113
|
Not recorded | 4NJ (5S)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxy-1-methyl-1,5-dihydro-2H-pyrrol-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5, 0.2 M sodium chloride, 25% (w/v) PEG 3350
|
Resolution 2.00 Å R-free 0.243 |
| 4ZGK Structure of Mdm2 with low molecular weight inhibitor. Deposited 2015-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–114（97 aa）
Fragment：UNP residues 18-114
|
Not recorded | 4NX (5R)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxyfuran-2(5H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；0.1 M HEPES pH 7.5 containing 30% PEG 1000
|
Resolution 2.00 Å R-free 0.247 |
| 4ZGK Structure of Mdm2 with low molecular weight inhibitor. Deposited 2015-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
18–114（97 aa）
Fragment：UNP residues 18-114
|
Not recorded | 4NX (5R)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxyfuran-2(5H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；0.1 M HEPES pH 7.5 containing 30% PEG 1000
|
Resolution 2.00 Å R-free 0.247 |
| 4ZYC Discovery of dihydroisoquinolinone derivatives as novel inhibitors of the p53-MDM2 interaction with a distinct binding mode: Hdm2 (MDM2) complexed with cpd5 Deposited 2015-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：N-TERMINAL DOMAIN, P53-BINDING DOMAIN, UNP residues 17-111
|
Mutation：L33E | 4SS (S)-2-(2-((2H-tetrazol-5-yl)methoxy)-4-methylphenyl)-1-(4-chlorophenyl)-6,7-diethoxy-1,2-dihydroisoquinolin-3(4H)-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；reservoir: 2.2M ammonium sulphate, 0.2M KNa tartrate, protein: 10mg/ml Hdm2 in 50mM TRIS pH 8.0, 200mM NaCl, 1mM TCEP, 10% glycerol, drop: 0.2ul reservoir + 0.2ul protein
|
Resolution 1.95 Å R-free 0.259 |
| 4ZYC Discovery of dihydroisoquinolinone derivatives as novel inhibitors of the p53-MDM2 interaction with a distinct binding mode: Hdm2 (MDM2) complexed with cpd5 Deposited 2015-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–111（95 aa）
Fragment：N-TERMINAL DOMAIN, P53-BINDING DOMAIN, UNP residues 17-111
|
Mutation：L33E | 4SS (S)-2-(2-((2H-tetrazol-5-yl)methoxy)-4-methylphenyl)-1-(4-chlorophenyl)-6,7-diethoxy-1,2-dihydroisoquinolin-3(4H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；reservoir: 2.2M ammonium sulphate, 0.2M KNa tartrate, protein: 10mg/ml Hdm2 in 50mM TRIS pH 8.0, 200mM NaCl, 1mM TCEP, 10% glycerol, drop: 0.2ul reservoir + 0.2ul protein
|
Resolution 1.95 Å R-free 0.259 |
| 4ZYC Discovery of dihydroisoquinolinone derivatives as novel inhibitors of the p53-MDM2 interaction with a distinct binding mode: Hdm2 (MDM2) complexed with cpd5 Deposited 2015-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
17–111（95 aa）
Fragment：N-TERMINAL DOMAIN, P53-BINDING DOMAIN, UNP residues 17-111
|
Mutation：L33E | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；reservoir: 2.2M ammonium sulphate, 0.2M KNa tartrate, protein: 10mg/ml Hdm2 in 50mM TRIS pH 8.0, 200mM NaCl, 1mM TCEP, 10% glycerol, drop: 0.2ul reservoir + 0.2ul protein
|
Resolution 1.95 Å R-free 0.259 |
| 4ZYF Discovery of NVP-CGM097 - a highly potent and selective MDM2 inhibitor undergoing phase 1 clinical trials in p53wt tumors: Hdm2 (MDM2) complexed with NVP-CGM097 Deposited 2015-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：N-TERMINAL DOMAIN, P53-BINDING DOMAIN, UNP residues 17-111
|
Not recorded | 4T4 (S)-1-(4-chlorophenyl)-7-isopropoxy-6-methoxy-2-(4-(methyl(((1r,4S)-4-(4-methyl-3-oxopiperazin-1-yl)cyclohexyl)methyl)amino)phenyl)-1,2-dihydroisoquinolin-3(4H)-one × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；reservoir: 2M AmSulfate, 0.1M cictric acid, pH4.5, protein: 7mg/ml Hdm2 in 50mM TRIS pH8.0, 200mM NaCl, 1mM TCEP, 10% glycerol, drop: 1ul reservoir + 1ul protein
|
Resolution 1.80 Å R-free 0.232 |
| 4ZYI Discovery of NVP-CGM097 - a highly potent and selective MDM2 inhibitor undergoing phase 1 clinical trials in p53wt tumors: Hdm2 (MDM2) complexed with cpd2 Deposited 2015-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：N-TERMINAL DOMAIN, P53-BINDING DOMAIN, UNP residues 17-111
|
Not recorded | 4TH (S)-7-((R)-sec-butoxy)-1-(4-chlorophenyl)-6-methoxy-2-(4-(methyl(pyridin-4-ylmethyl)amino)phenyl)-1,2-dihydroisoquinolin-3(4H)-one × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.7；298 K；reservoir: 2.2M AmmoniumSulfate, 0.1M cictric acid, pH4.7. protein: 7mg/ml Hdm2 in 50mM TRIS pH8.0, 200mM NaCl, 1mM TCEP, 10% glycerol. drop: 1ul reservoir + 1ul protein
|
Resolution 1.67 Å R-free 0.247 |
| 5AFG Structure of the Stapled Peptide Bound to Mdm2 Deposited 2015-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–108（92 aa）
Fragment：P53 BINDING DOMAIN (RESIDUES 17-108)
|
Mutation：YES | P07 1,8-DIETHYL-1,8-DIHYDRODIBENZO[3,4:7,8][1,2,3]TRIAZOLO[4',5':5,6]CYCLOOCTA[1,2-D][1,2,3]TRIAZOLE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.5；100 MM SODIUM ACETATE, 1 M AMMONIUM DI-HYDROGEN PHOSPHATE, PH 4.5
|
Resolution 1.90 Å R-free 0.226 |
| 5C5A Crystal Structure of HDM2 in complex with Nutlin-3a Deposited 2015-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
20–111（92 aa）
|
Not recorded | NUT 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 IOD IODIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Potassium iodide, 2.2M Ammonium Sulfate
|
Resolution 1.15 Å R-free 0.168 |
| 5C5A Crystal Structure of HDM2 in complex with Nutlin-3a Deposited 2015-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
20–111（92 aa）
|
Not recorded | NUT 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 IOD IODIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Potassium iodide, 2.2M Ammonium Sulfate
|
Resolution 1.15 Å R-free 0.168 |
| 5HMH HDM2 in complex with a 3,3-Disubstituted Piperidine Deposited 2016-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
21–116（96 aa）
|
Mutation：F55Y, Y76H | 62R 4-[2-(4-{[(2R,3S)-2-propyl-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}-3-{[5-(trifluoromethyl)thiophen-3-yl]oxy}piperidin-3-yl]carbonyl}piperazin-1-yl)phenoxy]butanoic acid × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.2；303 K；1.8-2.2 Ammonium sulfate
|
Resolution 1.79 Å R-free 0.239 |
| 5HMH HDM2 in complex with a 3,3-Disubstituted Piperidine Deposited 2016-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
21–116（96 aa）
|
Mutation：F55Y, Y76H | 62R 4-[2-(4-{[(2R,3S)-2-propyl-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}-3-{[5-(trifluoromethyl)thiophen-3-yl]oxy}piperidin-3-yl]carbonyl}piperazin-1-yl)phenoxy]butanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.2；303 K；1.8-2.2 Ammonium sulfate
|
Resolution 1.79 Å R-free 0.239 |
| 5HMH HDM2 in complex with a 3,3-Disubstituted Piperidine Deposited 2016-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
21–116（96 aa）
Chain B
21–116（96 aa）
|
Mutation：F55Y, Y76H Mutation：F55Y, Y76H | 62R 4-[2-(4-{[(2R,3S)-2-propyl-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}-3-{[5-(trifluoromethyl)thiophen-3-yl]oxy}piperidin-3-yl]carbonyl}piperazin-1-yl)phenoxy]butanoic acid × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.2；303 K；1.8-2.2 Ammonium sulfate
|
Resolution 1.79 Å R-free 0.239 |
| 5HMI HDM2 in complex with a 3,3-Disubstituted Piperidine Deposited 2016-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
24–122（99 aa）
|
Mutation：F55Y, Y76H | 62T {4-[2-(2-hydroxyethoxy)phenyl]piperazin-1-yl}[(2R,3S)-2-propyl-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}-3-{[5-(trifluoromethyl)thiophen-3-yl]oxy}piperidin-3-yl]methanone × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.2；303 K；1.8-2.2 M ammonium sulfate, 100 mM NaCitrate/Citric acid
|
Resolution 1.74 Å R-free 0.229 |
| 5HMI HDM2 in complex with a 3,3-Disubstituted Piperidine Deposited 2016-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
24–122（99 aa）
|
Mutation：F55Y, Y76H | 62T {4-[2-(2-hydroxyethoxy)phenyl]piperazin-1-yl}[(2R,3S)-2-propyl-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}-3-{[5-(trifluoromethyl)thiophen-3-yl]oxy}piperidin-3-yl]methanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.2；303 K；1.8-2.2 M ammonium sulfate, 100 mM NaCitrate/Citric acid
|
Resolution 1.74 Å R-free 0.229 |
| 5HMI HDM2 in complex with a 3,3-Disubstituted Piperidine Deposited 2016-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
24–122（99 aa）
Chain B
24–122（99 aa）
|
Mutation：F55Y, Y76H Mutation：F55Y, Y76H | 62T {4-[2-(2-hydroxyethoxy)phenyl]piperazin-1-yl}[(2R,3S)-2-propyl-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}-3-{[5-(trifluoromethyl)thiophen-3-yl]oxy}piperidin-3-yl]methanone × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.2；303 K；1.8-2.2 M ammonium sulfate, 100 mM NaCitrate/Citric acid
|
Resolution 1.74 Å R-free 0.229 |
| 5HMK HDM2 in complex with a 3,3-Disubstituted Piperidine Deposited 2016-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
23–131（109 aa）
|
Mutation：F55Y, Y76H | 62Q {4-[2-(2-hydroxyethoxy)phenyl]piperazin-1-yl}[(2R,3S)-2-propyl-3-[4-(trifluoromethyl)phenoxy]-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}piperidin-3-yl]methanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4；303 K；1.8-2.2 M ammonium sulfate, 100 mM Na Citrate/citric acid
|
Resolution 2.17 Å R-free 0.261 |
| 5HMK HDM2 in complex with a 3,3-Disubstituted Piperidine Deposited 2016-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
23–131（109 aa）
|
Mutation：F55Y, Y76H | 62Q {4-[2-(2-hydroxyethoxy)phenyl]piperazin-1-yl}[(2R,3S)-2-propyl-3-[4-(trifluoromethyl)phenoxy]-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}piperidin-3-yl]methanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4；303 K；1.8-2.2 M ammonium sulfate, 100 mM Na Citrate/citric acid
|
Resolution 2.17 Å R-free 0.261 |
| 5HMK HDM2 in complex with a 3,3-Disubstituted Piperidine Deposited 2016-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
23–131（109 aa）
Chain B
23–131（109 aa）
|
Mutation：F55Y, Y76H Mutation：F55Y, Y76H | 62Q {4-[2-(2-hydroxyethoxy)phenyl]piperazin-1-yl}[(2R,3S)-2-propyl-3-[4-(trifluoromethyl)phenoxy]-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}piperidin-3-yl]methanone × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4；303 K；1.8-2.2 M ammonium sulfate, 100 mM Na Citrate/citric acid
|
Resolution 2.17 Å R-free 0.261 |
| 5J7F Structure of MDM2 with low molecular weight inhibitor with aliphatic linker. Deposited 2016-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–125（125 aa）
Chain D
1–125（125 aa）
|
Not recorded | 6GG 4-({6-[(6-chloro-3-{1-[(4-chlorophenyl)methyl]-4-(4-fluorophenyl)-1H-imidazol-5-yl}-1H-indole-2-carbonyl)oxy]hexyl}amino)-4-oxobutanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5 with 0.2 M NaCl and 25% PEG 3350
|
Resolution 2.00 Å R-free 0.242 |
| 5J7F Structure of MDM2 with low molecular weight inhibitor with aliphatic linker. Deposited 2016-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
1–125（125 aa）
Chain C
1–125（125 aa）
|
Not recorded | 6GG 4-({6-[(6-chloro-3-{1-[(4-chlorophenyl)methyl]-4-(4-fluorophenyl)-1H-imidazol-5-yl}-1H-indole-2-carbonyl)oxy]hexyl}amino)-4-oxobutanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5 with 0.2 M NaCl and 25% PEG 3350
|
Resolution 2.00 Å R-free 0.242 |
| 5J7G Structure of MDM2 with low molecular weight inhibitor with aliphatic linker. Deposited 2016-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
18–125（108 aa）
Chain D
18–125（108 aa）
|
Not recorded | 6GG 4-({6-[(6-chloro-3-{1-[(4-chlorophenyl)methyl]-4-(4-fluorophenyl)-1H-imidazol-5-yl}-1H-indole-2-carbonyl)oxy]hexyl}amino)-4-oxobutanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M Na HEPES pH 7.5 with 10% isopropanol and 20% PEG 4000
|
Resolution 1.85 Å R-free 0.234 |
| 5J7G Structure of MDM2 with low molecular weight inhibitor with aliphatic linker. Deposited 2016-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
18–125（108 aa）
Chain C
18–125（108 aa）
|
Not recorded | 6GG 4-({6-[(6-chloro-3-{1-[(4-chlorophenyl)methyl]-4-(4-fluorophenyl)-1H-imidazol-5-yl}-1H-indole-2-carbonyl)oxy]hexyl}amino)-4-oxobutanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M Na HEPES pH 7.5 with 10% isopropanol and 20% PEG 4000
|
Resolution 1.85 Å R-free 0.234 |
| 5J7G Structure of MDM2 with low molecular weight inhibitor with aliphatic linker. Deposited 2016-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
18–125（108 aa）
Chain D
18–125（108 aa）
|
Not recorded | 6GG 4-({6-[(6-chloro-3-{1-[(4-chlorophenyl)methyl]-4-(4-fluorophenyl)-1H-imidazol-5-yl}-1H-indole-2-carbonyl)oxy]hexyl}amino)-4-oxobutanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M Na HEPES pH 7.5 with 10% isopropanol and 20% PEG 4000
|
Resolution 1.85 Å R-free 0.234 |
| 5LAV Novel Spiro[3H-indole-3,2 -pyrrolidin]-2(1H)-one Inhibitors of the MDM2-p53 Interaction: HDM2 (MDM2) in complex with compound 6b Deposited 2016-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
19–111（93 aa）
|
Not recorded | 6SK (3~{S},3'~{S},4'~{S})-4'-azanyl-6-chloranyl-3'-(3-chlorophenyl)-1'-(2,2-dimethylpropyl)spiro[1~{H}-indole-3,2'-pyrrolidine]-2-one × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；RESERVOIR SOLUTION : NULL
|
Resolution 1.73 Å R-free 0.273 |
| 5LAW Novel Spiro[3H-indole-3,2 -pyrrolidin]-2(1H)-one Inhibitors of the MDM2-p53 Interaction: HDM2 (MDM2) IN COMPLEX WITH COMPOUND 14 Deposited 2016-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
24–117（94 aa）
|
Not recorded | 6SJ 2-[(3~{S},3'~{a}~{S},6'~{S},6'~{a}~{S})-6-chloranyl-6'-(3-chlorophenyl)-4'-(cyclopropylmethyl)-2-oxidanylidene-spiro[1~{H}-indole-3,5'-3,3~{a},6,6~{a}-tetrahydro-2~{H}-pyrrolo[3,2-b]pyrrole]-1'-yl]ethanoic acid × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；RESERVOIR SOLUTION : NULL
|
Resolution 1.64 Å R-free 0.216 |
| 5LAY Discovery of New Natural-product-inspired Spiro-oxindole Compounds as Orally Active Inhibitors of the MDM2-p53 Interaction: HDM2 (MDM2) IN COMPLEX WITH COMPOUND 6g Deposited 2016-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：TRUNCATED N-TERMINAL DOMAIN
|
Not recorded | GOL GLYCEROL × 3 SO4 SULFATE ION × 1 6SS (3~{S},3'~{S},4'~{S},5'~{S})-4'-azanyl-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-[(3-ethoxyphenyl)methyl]-5'-methyl-spiro[1~{H}-indole-3,2'-pyrrolidine]-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；NULL
|
Resolution 2.71 Å R-free 0.292 |
| 5LAY Discovery of New Natural-product-inspired Spiro-oxindole Compounds as Orally Active Inhibitors of the MDM2-p53 Interaction: HDM2 (MDM2) IN COMPLEX WITH COMPOUND 6g Deposited 2016-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–111（95 aa）
Fragment：TRUNCATED N-TERMINAL DOMAIN
|
Not recorded | SO4 SULFATE ION × 1 6SS (3~{S},3'~{S},4'~{S},5'~{S})-4'-azanyl-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-[(3-ethoxyphenyl)methyl]-5'-methyl-spiro[1~{H}-indole-3,2'-pyrrolidine]-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；NULL
|
Resolution 2.71 Å R-free 0.292 |
| 5LAY Discovery of New Natural-product-inspired Spiro-oxindole Compounds as Orally Active Inhibitors of the MDM2-p53 Interaction: HDM2 (MDM2) IN COMPLEX WITH COMPOUND 6g Deposited 2016-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
17–111（95 aa）
Fragment：TRUNCATED N-TERMINAL DOMAIN
|
Not recorded | GOL GLYCEROL × 1 6SS (3~{S},3'~{S},4'~{S},5'~{S})-4'-azanyl-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-[(3-ethoxyphenyl)methyl]-5'-methyl-spiro[1~{H}-indole-3,2'-pyrrolidine]-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；NULL
|
Resolution 2.71 Å R-free 0.292 |
| 5LAY Discovery of New Natural-product-inspired Spiro-oxindole Compounds as Orally Active Inhibitors of the MDM2-p53 Interaction: HDM2 (MDM2) IN COMPLEX WITH COMPOUND 6g Deposited 2016-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
17–111（95 aa）
Fragment：TRUNCATED N-TERMINAL DOMAIN
|
Not recorded | SO4 SULFATE ION × 1 6SS (3~{S},3'~{S},4'~{S},5'~{S})-4'-azanyl-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-[(3-ethoxyphenyl)methyl]-5'-methyl-spiro[1~{H}-indole-3,2'-pyrrolidine]-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；NULL
|
Resolution 2.71 Å R-free 0.292 |
| 5LAY Discovery of New Natural-product-inspired Spiro-oxindole Compounds as Orally Active Inhibitors of the MDM2-p53 Interaction: HDM2 (MDM2) IN COMPLEX WITH COMPOUND 6g Deposited 2016-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
17–111（95 aa）
Fragment：TRUNCATED N-TERMINAL DOMAIN
|
Not recorded | GOL GLYCEROL × 1 SO4 SULFATE ION × 1 6SS (3~{S},3'~{S},4'~{S},5'~{S})-4'-azanyl-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-[(3-ethoxyphenyl)methyl]-5'-methyl-spiro[1~{H}-indole-3,2'-pyrrolidine]-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；NULL
|
Resolution 2.71 Å R-free 0.292 |
| 5LAY Discovery of New Natural-product-inspired Spiro-oxindole Compounds as Orally Active Inhibitors of the MDM2-p53 Interaction: HDM2 (MDM2) IN COMPLEX WITH COMPOUND 6g Deposited 2016-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
17–111（95 aa）
Fragment：TRUNCATED N-TERMINAL DOMAIN
|
Not recorded | 6SS (3~{S},3'~{S},4'~{S},5'~{S})-4'-azanyl-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-[(3-ethoxyphenyl)methyl]-5'-methyl-spiro[1~{H}-indole-3,2'-pyrrolidine]-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；NULL
|
Resolution 2.71 Å R-free 0.292 |
| 5LAZ Novel Spiro[3H-indole-3,2 -pyrrolidin]-2(1H)-one Inhibitors of the MDM2-p53 Interaction: HDM2 (MDM2) IN COMPLEX WITH COMPOUND BI-0252 Deposited 2016-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–111（94 aa）
|
Not recorded | 6ST 4-[(2~{R},3~{a}~{S},5~{S},6~{S},6~{a}~{S})-6'-chloranyl-6-(3-chloranyl-2-fluoranyl-phenyl)-4-(cyclopropylmethyl)-2'-oxidanylidene-spiro[1,2,3,3~{a},6,6~{a}-hexahydropyrrolo[3,2-b]pyrrole-5,3'-1~{H}-indole]-2-yl]benzoic acid × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；RESERVOIR SOLUTION : NULL
|
Resolution 1.66 Å R-free 0.205 |
| 5LN2 Discovery of a novel class of highly potent inhibitors of the p53-MDM2 interaction by structure-based design starting from a conformational argument Deposited 2016-08-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
23–117（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | 6ZT (4~{S})-5-[5-chloranyl-2-[2-(dimethylamino)ethoxy]phenyl]-4-(4-chloranyl-2-methyl-phenyl)-2-(2-methoxyphenyl)-3-propan-2-yl-4~{H}-pyrrolo[3,4-c]pyrazol-6-one × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；2.5M (NH4)2SO4, 0.1M NaCitrate
|
Resolution 1.58 Å R-free 0.247 |
| 5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
428–491（64 aa）
|
Not recorded | ZN ZINC ION × 4 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
|
Resolution 2.16 Å R-free 0.231 |
| 5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
428–491（64 aa）
|
Not recorded | ZN ZINC ION × 4 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
|
Resolution 2.16 Å R-free 0.231 |
| 5OAI Structure of MDM2 with low molecular weight inhibitor Deposited 2017-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–113（96 aa）
|
Not recorded | B5K 3-[(1~{R})-2-(~{tert}-butylamino)-1-[methanoyl-[[3,4,5-tris(fluoranyl)phenyl]methyl]amino]-2-oxidanylidene-ethyl]-6-chloranyl-1~{H}-indole-2-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.15 K；0.1 M Bis-Tris pH 6.5, 20% (w/v) PEG 5000 MME
|
Resolution 2.00 Å R-free 0.227 |
| 5OC8 HDM2 (17-111, WILD TYPE) COMPLEXED WITH NVP-HDM201 AT 1.56A Deposited 2017-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
23–117（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | 9QW (4~{S})-5-(5-chloranyl-1-methyl-2-oxidanylidene-pyridin-3-yl)-4-(4-chlorophenyl)-2-(2,4-dimethoxypyrimidin-5-yl)-3-propan-2-yl-4~{H}-pyrrolo[3,4-d]imidazol-6-one × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；3M AmSO4, 0.1M citrate
|
Resolution 1.56 Å R-free 0.260 |
| 5SWK Crystal structure of p53 epitope-scaffold based on a inhibitor of cysteine proteases in complex with human MDM2 Deposited 2016-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–150（150 aa）
Fragment：UNP residues 1-150
Chain B
1–150（150 aa）
Fragment：UNP residues 1-150
|
Not recorded | CL CHLORIDE ION × 7 SO4 SULFATE ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；0.1 M NaCl
0.1 M HEPES pH 7.5
1.6 M (NH4)2SO4
|
Resolution 1.92 Å R-free 0.249 |
| 5TRF MDM2 in complex with SAR405838 Deposited 2016-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
10–118（109 aa）
Fragment：residues 10-118
|
Not recorded | 7HC (2'S,3R,4'S,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(trans-4-hydroxycyclohexyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2m2M Ammonium Sulfate and 0.2M Lithium Nitrate
|
Resolution 2.10 Å R-free 0.208 |
| 5TRF MDM2 in complex with SAR405838 Deposited 2016-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
10–118（109 aa）
Fragment：residues 10-118
|
Not recorded | 7HC (2'S,3R,4'S,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(trans-4-hydroxycyclohexyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2m2M Ammonium Sulfate and 0.2M Lithium Nitrate
|
Resolution 2.10 Å R-free 0.208 |
| 5TRF MDM2 in complex with SAR405838 Deposited 2016-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
10–118（109 aa）
Fragment：residues 10-118
|
Not recorded | 7HC (2'S,3R,4'S,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(trans-4-hydroxycyclohexyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2m2M Ammonium Sulfate and 0.2M Lithium Nitrate
|
Resolution 2.10 Å R-free 0.208 |
| 5TRF MDM2 in complex with SAR405838 Deposited 2016-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
10–118（109 aa）
Fragment：residues 10-118
|
Not recorded | 7HC (2'S,3R,4'S,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(trans-4-hydroxycyclohexyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2m2M Ammonium Sulfate and 0.2M Lithium Nitrate
|
Resolution 2.10 Å R-free 0.208 |
| 5TRF MDM2 in complex with SAR405838 Deposited 2016-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
10–118（109 aa）
Fragment：residues 10-118
|
Not recorded | 7HC (2'S,3R,4'S,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(trans-4-hydroxycyclohexyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2m2M Ammonium Sulfate and 0.2M Lithium Nitrate
|
Resolution 2.10 Å R-free 0.208 |
| 5TRF MDM2 in complex with SAR405838 Deposited 2016-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
10–118（109 aa）
Fragment：residues 10-118
|
Not recorded | 7HC (2'S,3R,4'S,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(trans-4-hydroxycyclohexyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 2 SO4 SULFATE ION × 2 GOL GLYCEROL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2m2M Ammonium Sulfate and 0.2M Lithium Nitrate
|
Resolution 2.10 Å R-free 0.208 |
| 5TRF MDM2 in complex with SAR405838 Deposited 2016-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
10–118（109 aa）
Fragment：residues 10-118
Chain D
10–118（109 aa）
Fragment：residues 10-118
|
Not recorded | 7HC (2'S,3R,4'S,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(trans-4-hydroxycyclohexyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2m2M Ammonium Sulfate and 0.2M Lithium Nitrate
|
Resolution 2.10 Å R-free 0.208 |
| 5TRF MDM2 in complex with SAR405838 Deposited 2016-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
10–118（109 aa）
Fragment：residues 10-118
|
Not recorded | 7HC (2'S,3R,4'S,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(trans-4-hydroxycyclohexyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide × 2 SO4 SULFATE ION × 2 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2m2M Ammonium Sulfate and 0.2M Lithium Nitrate
|
Resolution 2.10 Å R-free 0.208 |
| 5UMM CRYSTAL STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH 12-MER PEPTIDE INHIBITOR M3 Deposited 2017-01-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M sodium cacodylate pH 5.5, 25% PEG (w/v) 4000
|
Resolution 1.65 Å R-free 0.231 |
| 5UMM CRYSTAL STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH 12-MER PEPTIDE INHIBITOR M3 Deposited 2017-01-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M sodium cacodylate pH 5.5, 25% PEG (w/v) 4000
|
Resolution 1.65 Å R-free 0.231 |
| 5VK0 Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI Deposited 2017-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
|
Resolution 1.80 Å R-free 0.247 |
| 5VK0 Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI Deposited 2017-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain S
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
|
Resolution 1.80 Å R-free 0.247 |
| 5VK0 Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI Deposited 2017-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain U
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
|
Resolution 1.80 Å R-free 0.247 |
| 5VK0 Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI Deposited 2017-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain W
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
|
Resolution 1.80 Å R-free 0.247 |
| 5VK0 Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI Deposited 2017-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
|
Resolution 1.80 Å R-free 0.247 |
| 5VK0 Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI Deposited 2017-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
|
Resolution 1.80 Å R-free 0.247 |
| 5VK0 Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI Deposited 2017-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
|
Resolution 1.80 Å R-free 0.247 |
| 5VK0 Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI Deposited 2017-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
|
Resolution 1.80 Å R-free 0.247 |
| 5VK0 Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI Deposited 2017-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain K
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
|
Resolution 1.80 Å R-free 0.247 |
| 5VK0 Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI Deposited 2017-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain M
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
|
Resolution 1.80 Å R-free 0.247 |
| 5VK0 Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI Deposited 2017-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain O
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
|
Resolution 1.80 Å R-free 0.247 |
| 5VK0 Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI Deposited 2017-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
25–109（85 aa）
Fragment：residues 25-109
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
|
Resolution 1.80 Å R-free 0.247 |
| 5WTS Green fluorescent protein linked MTide-02 inhibitor in complex with mdm2 Deposited 2016-12-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
6–125（120 aa）
Fragment：UNP residues 6-125
|
Not recorded | GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 2 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；288 K；0.2M sodium chloride, 0.1M Bis-Tris, 25% PEG3350
|
Resolution 3.00 Å R-free 0.244 |
| 5XXK Structure-activity studies of Mdm2/Mdm4-binding stapled peptides comprising non-natural amino acids Deposited 2017-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
6–125（120 aa）
Fragment：UNP residues 6-125
|
Mutation：M62A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.4；289 K；0.04M Citric acid, 0.06M Bis-Tris propane pH 6.4, 20% (v/v) PEG 3350
|
Resolution 1.66 Å R-free 0.209 |
| 5XXK Structure-activity studies of Mdm2/Mdm4-binding stapled peptides comprising non-natural amino acids Deposited 2017-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
6–125（120 aa）
Fragment：UNP residues 6-125
|
Mutation：M62A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.4；289 K；0.04M Citric acid, 0.06M Bis-Tris propane pH 6.4, 20% (v/v) PEG 3350
|
Resolution 1.66 Å R-free 0.209 |
| 5Z02 Crystal structure of HIS6-tagged Mdm2 with nutlin-3a Deposited 2017-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
24–112（89 aa）
Fragment：UNP residues 24-112
|
Not recorded | NUT 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.2 Ammonium acetate, 20% ammonium sulfate
|
Resolution 1.35 Å R-free 0.254 |
| 5ZXF The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a Deposited 2018-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
24–110（87 aa）
Fragment：UNP residues 24-110
|
Not recorded | NUT 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.2M NaOAc, 1.2M AmSO4, Seeding.
|
Resolution 1.25 Å R-free 0.243 |
| 6AAW Mdm2 in complex with a D amino Acid Containing Stapled Peptide Deposited 2018-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
6–125（120 aa）
Fragment：UNP residues 6-125
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20 % w/v Polyethylene glycol 8,000, 100 mM HEPES pH 7.5, 200 mM Ammonium sulfate, 10 % v/v 2-Propanol
|
Resolution 2.00 Å R-free 0.223 |
| 6GGN In vitro and in vivo characterization of a novel, highly potent p53-MDM2 inhibitor Deposited 2018-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | EYH (4~{S})-4-(4-chloranyl-2-methyl-phenyl)-5-(5-chloranyl-2-methyl-phenyl)-2-(2,4-dimethoxypyrimidin-5-yl)-3-propan-2-yl-4~{H}-pyrrolo[3,4-d]imidazol-6-one × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；2.5M (NH4)2SO4, 0.1M NaCitrate
|
Resolution 2.00 Å R-free 0.230 |
| 6H22 Crystal structure of Mdm2 bound to a stapled peptide Deposited 2018-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–108（92 aa）
|
Mutation：E69AK70A | FL5 12-(dimethylamino)-3,10-diethyl-N,N,N-trimethyl-3,10-dihydrodibenzo[3,4:7,8]cycloocta[1,2-d:5,6-d']bis([1,2,3]triazole)-5-aminium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292.15 K；1.1 M sodium malonate dibasic, 0.1 M HEPES pH 7.0, 0.5% v/v Jeffamine ED-2003
|
Resolution 2.01 Å R-free 0.238 |
| 6H22 Crystal structure of Mdm2 bound to a stapled peptide Deposited 2018-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
17–108（92 aa）
|
Mutation：E69AK70A | FL5 12-(dimethylamino)-3,10-diethyl-N,N,N-trimethyl-3,10-dihydrodibenzo[3,4:7,8]cycloocta[1,2-d:5,6-d']bis([1,2,3]triazole)-5-aminium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292.15 K；1.1 M sodium malonate dibasic, 0.1 M HEPES pH 7.0, 0.5% v/v Jeffamine ED-2003
|
Resolution 2.01 Å R-free 0.238 |
| 6HFA Crystal structure of hDM2 in complex with a C-terminal triurea capped peptide chimera foldamer. Deposited 2018-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
23–117（95 aa）
Fragment：residues 17-111
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；90 mM HEPES, 1.26 M Na Citrate, 10% glycerol. Cryo: +30% Glycerol
|
Resolution 1.79 Å R-free 0.238 |
| 6HFA Crystal structure of hDM2 in complex with a C-terminal triurea capped peptide chimera foldamer. Deposited 2018-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
23–117（95 aa）
Fragment：residues 17-111
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；90 mM HEPES, 1.26 M Na Citrate, 10% glycerol. Cryo: +30% Glycerol
|
Resolution 1.79 Å R-free 0.238 |
| 6I29 X-ray structure of the p53-MDM2 inhibitor NMI801 bound to HDM2 at 2.1A resolution Deposited 2018-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
23–117（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | H0W 6-chloranyl-3-[3-[(1~{S})-1-(4-chlorophenyl)ethyl]-5-phenyl-imidazol-4-yl]-~{N}-[2-[4-(2-oxidanylidene-1,3-oxazinan-3-yl)piperidin-1-yl]pyridin-3-yl]-1~{H}-indole-2-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 3.5；298 K；2.1M (NH4)SO4, 0.1M Citrate pH 3.5
|
Resolution 2.10 Å R-free 0.277 |
| 6I3S Crystal structure of MDM2 in complex with compound 13. Deposited 2018-11-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
18–111（94 aa）
|
Not recorded | H28 (3~{S},3'~{R},3'~{a}~{S},6'~{a}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-(cyclopropylmethyl)spiro[1~{H}-indole-3,2'-3~{a},6~{a}-dihydro-3~{H}-pyrrolo[3,4-b]pyrrole]-2,4'-dione × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；2.10 M (NH4)2SO4, 0.10 M Na acetate
|
Resolution 1.77 Å R-free 0.239 |
| 6IM9 MDM2 bound CueO-PM2 sensor Deposited 2018-10-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
6–125（120 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；4M sodium formate
|
Resolution 3.30 Å R-free 0.249 |
| 6KZU Macrocyclization of an all-D linear peptide improves target affinity and imparts cellular activity: A novel stapled alpha-helical peptide modality Deposited 2019-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
6–125（120 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；800 mM Sodium di-hydrogen phosphate, 800 mM di-Potassium hydrogen phosphate, 100 mM HEPES pH 7.5
|
Resolution 1.79 Å R-free 0.236 |
| 6Q96 HDM2 (17-111, WILD TYPE) COMPLEXED WITH COMPOUND 12 AT 1.8A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes Deposited 2018-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | HRE 4-[(4~{S})-5-(5-chloranyl-2-oxidanylidene-1~{H}-pyridin-3-yl)-2-[2-(dimethylamino)-4-methoxy-pyrimidin-5-yl]-6-oxidanylidene-3-propan-2-yl-4~{H}-pyrrolo[3,4-c]pyrazol-4-yl]benzenecarbonitrile × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；2.2M AmSO4, 0.2M citrate
|
Resolution 1.80 Å R-free 0.220 |
| 6Q96 HDM2 (17-111, WILD TYPE) COMPLEXED WITH COMPOUND 12 AT 1.8A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes Deposited 2018-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–111（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | HRE 4-[(4~{S})-5-(5-chloranyl-2-oxidanylidene-1~{H}-pyridin-3-yl)-2-[2-(dimethylamino)-4-methoxy-pyrimidin-5-yl]-6-oxidanylidene-3-propan-2-yl-4~{H}-pyrrolo[3,4-c]pyrazol-4-yl]benzenecarbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；2.2M AmSO4, 0.2M citrate
|
Resolution 1.80 Å R-free 0.220 |
| 6Q9H HDM2 (17-111, WILD TYPE) COMPLEXED WITH COMPOUND 11 AT 2.0A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes Deposited 2018-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | HRH (4~{S})-5-(3-chloranyl-2-fluoranyl-phenyl)-4-(4-chloranyl-2-methyl-phenyl)-3-propan-2-yl-1,4-dihydropyrrolo[3,4-c]pyrazol-6-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；2.2M AmSO4, 0.2M NH4PO4
|
Resolution 2.00 Å R-free 0.266 |
| 6Q9L HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 9 AT 1.13A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes Deposited 2018-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | HTZ [6-chloranyl-3-[3-[[4-chloranyl-2-(hydroxymethyl)phenyl]methyl]-5-phenyl-imidazol-4-yl]-1~{H}-indol-2-yl]-[(3~{S})-3-[3-(dimethylamino)propyl-methyl-amino]pyrrolidin-1-yl]methanone × 1 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；2.7M AmSO4, 0.2M NaI, 0.2M NaCl, 0.2M TRIS
|
Resolution 1.13 Å R-free 0.190 |
| 6Q9L HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 9 AT 1.13A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes Deposited 2018-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–111（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | HTZ [6-chloranyl-3-[3-[[4-chloranyl-2-(hydroxymethyl)phenyl]methyl]-5-phenyl-imidazol-4-yl]-1~{H}-indol-2-yl]-[(3~{S})-3-[3-(dimethylamino)propyl-methyl-amino]pyrrolidin-1-yl]methanone × 1 CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；2.7M AmSO4, 0.2M NaI, 0.2M NaCl, 0.2M TRIS
|
Resolution 1.13 Å R-free 0.190 |
| 6Q9O HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 10 AT 1.21A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes Deposited 2018-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | HU8 ~{N}-~{tert}-butyl-2-[4-chloranyl-2-[5-(3-chloranyl-4-fluoranyl-phenyl)-2-cyclohexyl-4-(1~{H}-1,2,3,4-tetrazol-5-yl)imidazol-1-yl]phenyl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；2.4M AmSO4, 0.1M NaCitrate, 0.2M NaCl, 0.1M TRIS
|
Resolution 1.21 Å R-free 0.156 |
| 6Q9O HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 10 AT 1.21A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes Deposited 2018-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–111（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | HU8 ~{N}-~{tert}-butyl-2-[4-chloranyl-2-[5-(3-chloranyl-4-fluoranyl-phenyl)-2-cyclohexyl-4-(1~{H}-1,2,3,4-tetrazol-5-yl)imidazol-1-yl]phenyl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；2.4M AmSO4, 0.1M NaCitrate, 0.2M NaCl, 0.1M TRIS
|
Resolution 1.21 Å R-free 0.156 |
| 6SQO Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2019-09-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
430–491（62 aa）
Chain D
430–491（62 aa）
|
Not recorded | ZN ZINC ION × 4 CL CHLORIDE ION × 4 NO3 NITRATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；292 K；0.1 M SPG, pH 7.0, 10% (w/v) PEG Smear Broad, 0.15 M NH4NO3
|
Resolution 1.41 Å R-free 0.173 |
| 6T2D Multicomponent Peptide Stapling as a Diversity-Driven Tool for the Development of Inhibitors of Protein-Protein Interactions Deposited 2019-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
25–109（85 aa）
|
Mutation：L33E | EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 DMS DIMETHYL SULFOXIDE × 1 M9E 2-(methylamino)-~{N}-[[4-[[2-(methylamino)ethanoylamino]methyl]phenyl]methyl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1M TRIS pH 8, 0.2M Ammonium Sulfate, 30% PEG-3350
|
Resolution 1.80 Å R-free 0.226 |
| 6T2E Multicomponent Peptide Stapling as a Diversity-Driven Tool for the Development of Inhibitors of Protein-Protein Interactions Deposited 2019-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
25–109（85 aa）
|
Mutation：L33E | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.2；295 K；0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH8.2
|
Resolution 2.40 Å R-free 0.290 |
| 6T2F Multicomponent Peptide Stapling as a Diversity-Driven Tool for the Development of Inhibitors of Protein-Protein Interactions Deposited 2019-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
25–109（85 aa）
|
Mutation：L33E | M9H 2-(methylamino)-~{N}-[[3-[[2-(methylamino)ethanoylamino]methyl]phenyl]methyl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1M TRIS pH 8, 0.2M Trimethyl N-oxide dihydrate, 20% PEG-2000
|
Resolution 2.09 Å R-free 0.272 |
| 6Y4Q Structure of a stapled peptide bound to MDM2 Deposited 2020-02-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–108（92 aa）
|
Mutation：E69A, K70A | O9E ~{N}-[(1-ethyl-1,2,3-triazol-4-yl)methyl]-~{N},5-dimethyl-4-[2-[2-methyl-5-[methyl-[(1-propyl-1,2,3-triazol-4-yl)methyl]carbamoyl]thiophen-3-yl]cyclopenten-1-yl]thiophene-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；10% w/v PEG 8000 (precipitant), 0.1 M Tris-HCl pH 7.0 (buffer), 0.2 M Magnesium chloride hexahydrate (salt)
|
Resolution 1.63 Å R-free 0.229 |
| 6Y4Q Structure of a stapled peptide bound to MDM2 Deposited 2020-02-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
17–108（92 aa）
|
Mutation：E69A, K70A | O9E ~{N}-[(1-ethyl-1,2,3-triazol-4-yl)methyl]-~{N},5-dimethyl-4-[2-[2-methyl-5-[methyl-[(1-propyl-1,2,3-triazol-4-yl)methyl]carbamoyl]thiophen-3-yl]cyclopenten-1-yl]thiophene-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；10% w/v PEG 8000 (precipitant), 0.1 M Tris-HCl pH 7.0 (buffer), 0.2 M Magnesium chloride hexahydrate (salt)
|
Resolution 1.63 Å R-free 0.229 |
| 7AD0 X-ray structure of Mdm2 with modified p53 peptide Deposited 2020-09-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
24–113（90 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M Bis-Tris pH 5.5 with 0.2 M NaCl and 25% PEG 3350
|
Resolution 2.07 Å R-free 0.238 |
| 7AD0 X-ray structure of Mdm2 with modified p53 peptide Deposited 2020-09-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
24–113（90 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M Bis-Tris pH 5.5 with 0.2 M NaCl and 25% PEG 3350
|
Resolution 2.07 Å R-free 0.238 |
| 7AD0 X-ray structure of Mdm2 with modified p53 peptide Deposited 2020-09-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
24–113（90 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M Bis-Tris pH 5.5 with 0.2 M NaCl and 25% PEG 3350
|
Resolution 2.07 Å R-free 0.238 |
| 7AD0 X-ray structure of Mdm2 with modified p53 peptide Deposited 2020-09-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
24–113（90 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M Bis-Tris pH 5.5 with 0.2 M NaCl and 25% PEG 3350
|
Resolution 2.07 Å R-free 0.238 |
| 7AD0 X-ray structure of Mdm2 with modified p53 peptide Deposited 2020-09-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
24–113（90 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M Bis-Tris pH 5.5 with 0.2 M NaCl and 25% PEG 3350
|
Resolution 2.07 Å R-free 0.238 |
| 7AD0 X-ray structure of Mdm2 with modified p53 peptide Deposited 2020-09-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
24–113（90 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M Bis-Tris pH 5.5 with 0.2 M NaCl and 25% PEG 3350
|
Resolution 2.07 Å R-free 0.238 |
| 7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
419–491（73 aa）
Chain DDD
419–491（73 aa）
|
Mutation：G443T Mutation：G443T | CL CHLORIDE ION × 3 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
|
Resolution 1.56 Å R-free 0.185 |
| 7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain AAA
419–491（73 aa）
|
Mutation：G443T | CL CHLORIDE ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
|
Resolution 1.56 Å R-free 0.185 |
| 7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain DDD
419–491（73 aa）
|
Mutation：G443T | CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
|
Resolution 1.56 Å R-free 0.185 |
| 7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
419–491（73 aa）
Chain DDD
419–491（73 aa）
|
Mutation：G443T Mutation：G443T | CL CHLORIDE ION × 2 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
|
Resolution 2.07 Å R-free 0.266 |
| 7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain AAA
419–491（73 aa）
|
Mutation：G443T | CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
|
Resolution 2.07 Å R-free 0.266 |
| 7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain DDD
419–491（73 aa）
|
Mutation：G443T | CL CHLORIDE ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
|
Resolution 2.07 Å R-free 0.266 |
| 7AYE Crystal structure of the computationally designed chemically disruptable heterodimer LD6-MDM2 Deposited 2020-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
23–131（109 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；1.5 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6.5
|
Resolution 2.95 Å R-free 0.260 |
| 7BIR Inhibitor of MDM2-p53 Interaction Deposited 2021-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–109（93 aa）
|
Not recorded | SO4 SULFATE ION × 2 TUZ 1-[[(1~{R})-2-[(5-chloranylpyridin-2-yl)methyl]-1-(4-chlorophenyl)-7-fluoranyl-3-oxidanylidene-5-(2-oxidanylpropan-2-yl)isoindol-1-yl]oxymethyl]cyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；2M (NH4)2SO4
5% PEG 400
.1M pH=6.5 Na MES/HCl
|
Resolution 2.02 Å R-free 0.243 |
| 7BIT Inhibitor of MDM2-p53 Interaction Deposited 2021-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–125（109 aa）
|
Not recorded | SO4 SULFATE ION × 1 TV5 (3~{R})-2-[(5-chloranylpyridin-2-yl)methyl]-3-(4-chlorophenyl)-4-fluoranyl-3-[(1-oxidanylcyclopropyl)methoxy]-6-(2-oxidanylpropan-2-yl)isoindol-1-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；1.5M (NH4)2SO4
15% Glycerol
.1M pH=8.5 Tris Cl/NaOH
|
Resolution 2.13 Å R-free 0.307 |
| 7BIV Inhibitor of MDM2-p53 Interaction Deposited 2021-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–109（93 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 2 TUW 6-[[(1~{R})-1-(4-chlorophenyl)-7-fluoranyl-1-[[1-(hydroxymethyl)cyclopropyl]methoxy]-3-oxidanylidene-5-(2-oxidanylpropan-2-yl)isoindol-2-yl]methyl]pyridine-3-carbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；2.4M (NH4)2SO4
.1M pH=6 MES/NaOH
|
Resolution 1.64 Å R-free 0.237 |
| 7BJ0 Inhibitor of MDM2-p53 Interaction Deposited 2021-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
17–125（109 aa）
Chain B
17–125（109 aa）
|
Not recorded | TVH (3~{R})-4-chloranyl-3-(4-chlorophenyl)-3-[[1-(hydroxymethyl)cyclopropyl]methoxy]-2-[(4-nitrophenyl)methyl]isoindol-1-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；2.2M (NH4)2SO4
|
Resolution 2.00 Å R-free 0.211 |
| 7BJ6 Inhibitor of MDM2-p53 Interaction Deposited 2021-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–109（93 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 3 TVK (3~{R})-2-[(5-chloranylpyridin-2-yl)methyl]-3-(4-chlorophenyl)-4-fluoranyl-3-[[1-(hydroxymethyl)cyclopropyl]methoxy]-6-(2-oxidanylpropan-2-yl)isoindol-1-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；2.4M (NH4)2SO4
.1M pH=6 MES/NaOH
|
Resolution 1.59 Å R-free 0.258 |
| 7BMG Inhibitor of MDM2-p53 Interaction Deposited 2021-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–109（93 aa）
|
Mutation：E69A,K70A | EDO 1,2-ETHANEDIOL × 3 U3Z (3~{R})-3-(4-chlorophenyl)-2-[(4-ethynylphenyl)methyl]-3-[[1-(hydroxymethyl)cyclopropyl]methoxy]-6-(2-oxidanylpropan-2-yl)isoindol-1-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；2.2M (NH4)2SO4
|
Resolution 1.83 Å R-free 0.251 |
| 7KJM CRYSTAL STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH D-PEPTIDE INHIBITOR (DPMI-OMEGA) Deposited 2020-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
25–109（85 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 IPA ISOPROPYL ALCOHOL × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；30% isopropanol, 15% PEG 8000, 0.1 M imidazole pH 6.5
|
Resolution 1.40 Å R-free 0.210 |
| 7KJM CRYSTAL STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH D-PEPTIDE INHIBITOR (DPMI-OMEGA) Deposited 2020-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
25–109（85 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；30% isopropanol, 15% PEG 8000, 0.1 M imidazole pH 6.5
|
Resolution 1.40 Å R-free 0.210 |
| 7NA1 HDM2 in complex with compound 2 Deposited 2021-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
23–131（109 aa）
|
Mutation：F55Y,Y76H | 1GI 8-(1-benzothiophen-5-yl)-7-[(4-chlorophenyl)methyl]-6-{[(1R)-1-cyclopropylethyl]amino}-7H-purine-2-carboxylic acid × 1 SO4 SULFATE ION × 1 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；2 M ammonium sulfate, 100 mM citrate pH 3.5
|
Resolution 2.30 Å R-free 0.354 |
| 7NA1 HDM2 in complex with compound 2 Deposited 2021-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
23–131（109 aa）
|
Mutation：F55Y,Y76H | 1GI 8-(1-benzothiophen-5-yl)-7-[(4-chlorophenyl)methyl]-6-{[(1R)-1-cyclopropylethyl]amino}-7H-purine-2-carboxylic acid × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；285 K；2 M ammonium sulfate, 100 mM citrate pH 3.5
|
Resolution 2.30 Å R-free 0.354 |
| 7NA2 HDM2 in complex with compound 56 Deposited 2021-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
23–131（109 aa）
|
Not recorded | 1I0 3-[4-(5-chloropyridin-3-yl)-2-[(4aR,7aR)-hexahydrocyclopenta[b][1,4]oxazin-4(4aH)-yl]-3-{[(1r,4R)-4-methylcyclohexyl]methyl}-3H-imidazo[4,5-c]pyridin-6-yl]-1,2,4-oxadiazol-5(4H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；undisclosed
|
Resolution 1.86 Å R-free 0.259 |
| 7NA2 HDM2 in complex with compound 56 Deposited 2021-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
23–131（109 aa）
|
Not recorded | 1I0 3-[4-(5-chloropyridin-3-yl)-2-[(4aR,7aR)-hexahydrocyclopenta[b][1,4]oxazin-4(4aH)-yl]-3-{[(1r,4R)-4-methylcyclohexyl]methyl}-3H-imidazo[4,5-c]pyridin-6-yl]-1,2,4-oxadiazol-5(4H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；undisclosed
|
Resolution 1.86 Å R-free 0.259 |
| 7NA3 HDM2 in complex with compound 62 Deposited 2021-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
23–131（109 aa）
|
Not recorded | 1I3 3-[4-(5-chloropyridin-3-yl)-2-[(2S)-1-methoxypropan-2-yl]-3-{(1R)-1-[(1r,4R)-4-methylcyclohexyl]ethyl}-3H-imidazo[4,5-c]pyridin-6-yl]-1,2,4-oxadiazol-5(4H)-one × 1 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；undisclosed
|
Resolution 2.21 Å R-free 0.219 |
| 7NA4 HDM2 in complex with compound 63 Deposited 2021-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
23–131（109 aa）
|
Not recorded | 1I9 3-[4-(5-chloropyridin-3-yl)-2-[(R)-cyclopropyl(ethoxy)methyl]-3-{(1R)-1-[(1r,4R)-4-methylcyclohexyl]ethyl}-3H-imidazo[4,5-c]pyridin-6-yl]-1,2,4-oxadiazol-5(4H)-one × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；undisclosed
|
Resolution 1.84 Å R-free 0.217 |
| 7NUS X-RAY STRUCTURE OF HDM2/CMR19 AT 1.45A: Discovery, X-ray structure and CPP-conjugation enabled uptake of p53/MDM2 macrocyclic peptide inhibitors Deposited 2021-03-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–111（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；2.2 M AmSO4, 0.2 M NaAcetate
|
Resolution 1.45 Å R-free 0.197 |
| 7NUS X-RAY STRUCTURE OF HDM2/CMR19 AT 1.45A: Discovery, X-ray structure and CPP-conjugation enabled uptake of p53/MDM2 macrocyclic peptide inhibitors Deposited 2021-03-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
17–111（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；2.2 M AmSO4, 0.2 M NaAcetate
|
Resolution 1.45 Å R-free 0.197 |
| 7NUS X-RAY STRUCTURE OF HDM2/CMR19 AT 1.45A: Discovery, X-ray structure and CPP-conjugation enabled uptake of p53/MDM2 macrocyclic peptide inhibitors Deposited 2021-03-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
17–111（95 aa）
Fragment：N-terminal domain, p53 binding domain
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；2.2 M AmSO4, 0.2 M NaAcetate
|
Resolution 1.45 Å R-free 0.197 |
| 7QDQ Crystal Structure of HDM2 in complex with Caylin-1 Deposited 2021-11-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
20–111（92 aa）
|
Not recorded | CL CHLORIDE ION × 3 NA SODIUM ION × 2 SO4 SULFATE ION × 1 AU0 Caylin-1 × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；2.8M Ammonium Sulfate, 100mM MES
|
Resolution 1.26 Å R-free 0.216 |
| 8AEU Structure of hMDM2 in complex with Nutlin-3a-aa Deposited 2022-07-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
18–113（96 aa）
|
Not recorded | BME BETA-MERCAPTOETHANOL × 2 M0L 4-[[(4~{S},5~{R})-4,5-bis(4-chlorophenyl)-2-(4-methoxy-2-propan-2-yloxy-phenyl)-4,5-dihydroimidazol-1-yl]carbonyl]-3-methylidene-piperazin-2-one × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M magnesium chloride hexahydrate, 0.05 M Tris hydrochloride pH 7.6, 1.6 M ammonium sulfate
|
Resolution 2.00 Å R-free 0.240 |
| 8BGU human MDM2-5S RNP Deposited 2022-10-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric |
Chain F
1–491（491 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8EI9 Crystal structure of beta-catenin and the MDM2 p53-binding domain in complex with H332, a Helicon Polypeptide Deposited 2022-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
17–111（95 aa）
Fragment：P53 binding domain
|
Not recorded | WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M MES Sodium Salt pH6.5, 10% v/v 2-Propanol, 25% v/v PEG 400
|
Resolution 3.90 Å R-free 0.315 |
| 8EIA Crystal structure of beta-catenin and the MDM2 p53-binding domain in complex with H333, a Helicon Polypeptide Deposited 2022-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
17–111（95 aa）
Fragment：P53 binding domain
|
Not recorded | WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M Potassium chloride, 0.1 M HEPES pH 7, 15% w/v PEG 5000 MME
|
Resolution 3.60 Å R-free 0.373 |
| 8EIB Crystal structure of beta-catenin and the MDM2 p53-binding domain in complex with H329, a Helicon Polypeptide Deposited 2022-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
17–111（95 aa）
Fragment：P53 binding domain
|
Not recorded | WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.2 M Calcium acetate pH 7.5, 20% w/v PEG 3350
|
Resolution 3.76 Å R-free 0.298 |
| 8EIC Crystal structure of beta-catenin and the MDM2 p53-binding domain in complex with H330, a Helicon Polypeptide Deposited 2022-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
17–111（95 aa）
Fragment：P53 binding domain
|
Not recorded | WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；4M Sodium formate
|
Resolution 2.62 Å R-free 0.269 |
| 8F0Z Structure of the MDM2 P53 binding domain in complex with H101, an all-D Helicon Polypeptide Deposited 2022-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–111（95 aa）
|
Not recorded | CL CHLORIDE ION × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；3.5 M Sodium Formate pH 7.0
|
Resolution 1.61 Å R-free 0.242 |
| 8F10 Structure of the MDM2 P53 binding domain in complex with H102, an all-D Helicon Polypeptide Deposited 2022-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–111（95 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 WHL N,N'-(1,4-phenylene)diacetamide × 1 IMD IMIDAZOLE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.01 M tri-Sodium citrate, 33 % w/v PEG 6000
|
Resolution 1.28 Å R-free 0.167 |
| 8F12 Structure of the MDM2 P53 binding domain in complex with H103, an all-D Helicon Polypeptide Deposited 2022-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–111（95 aa）
|
Not recorded | SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；3.2 M Ammonium sulfate, 0.1 M Citrate pH 5.0
|
Resolution 1.86 Å R-free 0.241 |
| 8F13 Structure of the MDM2 P53 binding domain in complex with H103, an all-D Helicon Polypeptide, alternative C-terminus Deposited 2022-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–111（95 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 6 SO4 SULFATE ION × 1 DMS DIMETHYL SULFOXIDE × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Potassium sodium tartrate, 0.1 M tri-Sodium citrate pH 5.6, 2.0 M Ammonium sulfate
|
Resolution 1.40 Å R-free 0.208 |
| 8GCG MDM2 bound to inhibitor Deposited 2023-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
17–125（109 aa）
Fragment：residues 17-125
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；2.0 M Ammonium sulfate
0.2M Sodium/Potassium Tartrate
|
Resolution 1.47 Å R-free 0.234 |
| 8J81 MDM2 bound with a peptoid Deposited 2023-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–111（95 aa）
|
Not recorded | UAC (2S)-2-[[(2S)-2-[(6-chloranyl-1H-indol-3-yl)methyl-[(2S)-2-[[(2S)-2-[ethanoyl-(phenylmethyl)amino]propanoyl]-methyl-amino]propanoyl]amino]propanoyl]-methyl-amino]-N-(3,3-dimethylbutyl)-N-[(2S)-1-oxidanylidene-1-piperazin-1-yl-propan-2-yl]propanamide × 1 CL CHLORIDE ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；1M Sodium Acetate trihydrate pH4.5, 3.0 M Sodium Chrolide. Peptoid dissolved in DMSO was included. The final DMSO concentration was 2.4%
|
Resolution 1.35 Å R-free 0.190 |
| 8P0D Human 14-3-3 sigma in complex with human MDM2 peptide Deposited 2023-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
161–191（31 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；1 M HEPES pH 7.4 to 7.6, 0.19 M CaCl2, 30 to 31 % PEG 400, 5 % glycerol
|
Resolution 1.31 Å R-free 0.204 |
| 8PWC Crystal structure of MDM2 with Brigimadlin Deposited 2023-07-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
17–125（109 aa）
|
Not recorded | G7I Brigimadlin × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；22% PEG 3350, 0.1M sodium sulphate, 10 mM manganes chloride
|
Resolution 1.46 Å R-free 0.226 |
| 8PWC Crystal structure of MDM2 with Brigimadlin Deposited 2023-07-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
17–125（109 aa）
|
Not recorded | G7I Brigimadlin × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；22% PEG 3350, 0.1M sodium sulphate, 10 mM manganes chloride
|
Resolution 1.46 Å R-free 0.226 |
| 8PWC Crystal structure of MDM2 with Brigimadlin Deposited 2023-07-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
17–125（109 aa）
|
Not recorded | G7I Brigimadlin × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；22% PEG 3350, 0.1M sodium sulphate, 10 mM manganes chloride
|
Resolution 1.46 Å R-free 0.226 |
| 9CDZ Crystal Structure of MDM2-Peptide Complex Deposited 2024-06-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
18–125（108 aa）
|
Mutation：E52A, K53A | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30 % w/v polyacylate 5100, sodium salt, 10% ethanol and 0.1 M MES-NaOH
|
Resolution 1.72 Å R-free 0.270 |
| 9CDZ Crystal Structure of MDM2-Peptide Complex Deposited 2024-06-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
18–125（108 aa）
|
Mutation：E52A, K53A | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30 % w/v polyacylate 5100, sodium salt, 10% ethanol and 0.1 M MES-NaOH
|
Resolution 1.72 Å R-free 0.270 |
| 9FQL Crystal structure of hDM2 in complex with a peptidic ligand containing a di-urea insert. Deposited 2024-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
25–110（86 aa）
Fragment：residues 17-111
Chain B
25–110（86 aa）
Fragment：residues 17-111
|
Not recorded | PO4 PHOSPHATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8.5；298 K；1 M Na2HPO4/K2HPO4 pH 6.9, 30% Glycerol
|
Resolution 2.00 Å R-free 0.248 |
| 9FQL Crystal structure of hDM2 in complex with a peptidic ligand containing a di-urea insert. Deposited 2024-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
25–110（86 aa）
Fragment：residues 17-111
Chain F
25–110（86 aa）
Fragment：residues 17-111
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8.5；298 K；1 M Na2HPO4/K2HPO4 pH 6.9, 30% Glycerol
|
Resolution 2.00 Å R-free 0.248 |
| 9FQL Crystal structure of hDM2 in complex with a peptidic ligand containing a di-urea insert. Deposited 2024-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain I
25–110（86 aa）
Fragment：residues 17-111
Chain J
25–110（86 aa）
Fragment：residues 17-111
|
Not recorded | PO4 PHOSPHATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8.5；298 K；1 M Na2HPO4/K2HPO4 pH 6.9, 30% Glycerol
|
Resolution 2.00 Å R-free 0.248 |
| 9GFC HDM2 complexed with stapled peptide-like ligand Deposited 2024-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
25–110（86 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Ammonium Sulfate 2.5M + Tris 0.1M pH8.5
|
Resolution 2.50 Å R-free 0.318 |
| 9GFC HDM2 complexed with stapled peptide-like ligand Deposited 2024-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
25–110（86 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Ammonium Sulfate 2.5M + Tris 0.1M pH8.5
|
Resolution 2.50 Å R-free 0.318 |
| 9GFC HDM2 complexed with stapled peptide-like ligand Deposited 2024-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
25–110（86 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Ammonium Sulfate 2.5M + Tris 0.1M pH8.5
|
Resolution 2.50 Å R-free 0.318 |
| 9GFC HDM2 complexed with stapled peptide-like ligand Deposited 2024-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
25–110（86 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Ammonium Sulfate 2.5M + Tris 0.1M pH8.5
|
Resolution 2.50 Å R-free 0.318 |
| 9GFK human MDM2 complex with stapled foldamer Deposited 2024-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
17–111（95 aa）
Fragment：TRUNCATED N-TERMINAL DOMAIN
Chain B
17–111（95 aa）
Fragment：TRUNCATED N-TERMINAL DOMAIN
Chain C
17–111（95 aa）
Fragment：TRUNCATED N-TERMINAL DOMAIN
Chain D
17–111（95 aa）
Fragment：TRUNCATED N-TERMINAL DOMAIN
|
Not recorded | SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；290 K；Ammonium Sulfate 2.5M + MES 0.1M pH5.5
|
Resolution 1.84 Å R-free 0.239 |
142 other PDB entries and 278 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | MDM2_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–85； UniProt 25–109 Author chain B； PDBConstruct 1–85； UniProt 25–109 Author chain C； PDBConstruct 1–85； UniProt 25–109 |
