Glucose-induced degradation protein 4 homolog
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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 124–289 | Fragment：Residues 124-289 | 98C N,N~2~-bis[(4-methoxyphenyl)methyl]glycinamide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M Tris-HCl 8.5, 30% PEG3350, 0.2 M MgCl2 | Resolution 2.21 Å R-free 0.278 |
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 8V1P | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 6CCR Selenomethionyl derivative of a GID4 fragment Deposited 2018-02-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–300（185 aa）
Fragment：residues 116-300
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 36 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；10% 2-propanol, 20% PEG4K and 0.1M Na-HEPES
|
Resolution 1.60 Å R-free 0.187 |
| 6CCT Fragment of GID4 in complex with a short peptide Deposited 2018-02-07 | Different construct 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
124–289（166 aa）
Fragment：residues 124-289
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 2% Tacsimate pH 7.0 and 0.1M HEPES pH 7.5
|
Resolution 2.40 Å R-free 0.260 |
| 6CCU Complex between a GID4 fragment and a short peptide Deposited 2018-02-07 | Different construct 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
116–300（185 aa）
|
Not recorded | UNX UNKNOWN LIGAND × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350 and 0.03M Citric acid
|
Resolution 1.75 Å R-free 0.236 |
| 6CD8 Complex of GID4 fragment with short peptide Deposited 2018-02-08 | Different construct 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
124–289（166 aa）
Fragment：residues 124-289
|
Not recorded | UNX UNKNOWN LIGAND × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000 and 0.1M KSCN
|
Resolution 1.60 Å R-free 0.224 |
| 6CD8 Complex of GID4 fragment with short peptide Deposited 2018-02-08 | Different construct 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
124–289（166 aa）
Fragment：residues 124-289
|
Not recorded | UNX UNKNOWN LIGAND × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000 and 0.1M KSCN
|
Resolution 1.60 Å R-free 0.224 |
| 6CD9 GID4 in complex with a peptide Deposited 2018-02-08 | Different construct 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
124–289（166 aa）
Fragment：residues 124-289
|
Not recorded | UNX UNKNOWN LIGAND × 46 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；24% PEG3350, 2.8% Tacsimate pH 7.0 and 0.1M HEPES pH 7.5
|
Resolution 1.55 Å R-free 0.193 |
| 6CDC GID4 in complex with a tetrapeptide Deposited 2018-02-08 | Different construct 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
124–289（166 aa）
Fragment：residues 124-289
|
Not recorded | UNX UNKNOWN LIGAND × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；30%PEG3350, 0.2M NaCl and 0.1M Tris pH 8.5
|
Resolution 1.75 Å R-free 0.239 |
| 6CDG GID4 fragment in complex with a peptide Deposited 2018-02-08 | Different construct 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
124–289（166 aa）
Fragment：residues 124-289
|
Not recorded | UNX UNKNOWN LIGAND × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2M sodium bromide
|
Resolution 1.60 Å R-free 0.248 |
| 6WZX GID4 in complex with IGLWKS peptide Deposited 2020-05-14 | Different construct 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
124–289（166 aa）
|
Not recorded | UNX UNKNOWN LIGAND × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；20% (w/v) PEG 3350 and 8% (v/v) Tacsimate pH 7.0
|
Resolution 1.75 Å R-free 0.227 |
| 6WZX GID4 in complex with IGLWKS peptide Deposited 2020-05-14 | Different construct 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
124–289（166 aa）
|
Not recorded | UNX UNKNOWN LIGAND × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；20% (w/v) PEG 3350 and 8% (v/v) Tacsimate pH 7.0
|
Resolution 1.75 Å R-free 0.227 |
| 6WZZ GID4 in complex with VGLWKS peptide Deposited 2020-05-14 | Different construct 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
124–289（166 aa）
|
Not recorded | UNX UNKNOWN LIGAND × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.03 M Citric acid, pH 7.6 and 20% (w/v) PEG 3350
|
Resolution 1.60 Å R-free 0.220 |
| 7NSC Substrate receptor scaffolding module of human CTLH E3 ubiquitin ligase Deposited 2021-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
1–300（300 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7Q4Y human Gid4 bound to a Gly/N-peptide Deposited 2021-11-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
100–300（201 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；18% PEG 3350, 0.2 M ammonium nitrate, 0.1 M Bis-Tris pH 7
|
Resolution 3.08 Å R-free 0.265 |
| 7Q4Y human Gid4 bound to a Gly/N-peptide Deposited 2021-11-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
100–300（201 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；18% PEG 3350, 0.2 M ammonium nitrate, 0.1 M Bis-Tris pH 7
|
Resolution 3.08 Å R-free 0.265 |
| 7Q50 human Gid4 bound to a Phe/N-peptide Deposited 2021-11-02 | Different construct 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
121–290（170 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.1 M Sodium malonate, 0.3% Jeffamine ED-2001 pH 7, 0.1 M HEPES pH 7
|
Resolution 3.16 Å R-free 0.293 |
| 7SLZ CRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH BPF023596 Deposited 2021-10-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | 9QU N-[(1s,4s)-4-(1H-benzimidazol-2-yl)cyclohexyl]-N~2~-[(1H-indol-2-yl)methyl]glycinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；35% PEG 3350, 0.2M CaAC
|
Resolution 1.97 Å R-free 0.246 |
| 7U3E GID4 in complex with compound 1 Deposited 2022-02-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | L4O tert-butyl (1S,4S)-2,5-diazabicyclo[2.2.1]heptane-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；17% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium acetate
|
Resolution 1.85 Å R-free 0.234 |
| 7U3E GID4 in complex with compound 1 Deposited 2022-02-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
124–289（166 aa）
|
Not recorded | L4O tert-butyl (1S,4S)-2,5-diazabicyclo[2.2.1]heptane-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；17% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium acetate
|
Resolution 1.85 Å R-free 0.234 |
| 7U3F GID4 in complex with compound 4 Deposited 2022-02-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | GOL GLYCEROL × 1 L5L (4R)-4-(4-methoxyphenyl)-4,5,6,7-tetrahydrothieno[3,2-c]pyridine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG5000 MME, 0.1 M Bis-tris
|
Resolution 2.30 Å R-free 0.262 |
| 7U3G GID4 in complex with compound 67 Deposited 2022-02-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | L6F (1R)-1-phenyl-1,2,3,4-tetrahydroisoquinolin-5-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium acetate
|
Resolution 2.24 Å R-free 0.240 |
| 7U3H GID4 in complex with compound 7 Deposited 2022-02-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | L6O (5R)-N-(4-fluorophenyl)-5-methyl-4,5-dihydro-1,3-thiazol-2-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；14% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium formate
|
Resolution 1.80 Å R-free 0.224 |
| 7U3I GID4 in complex with compound 16 Deposited 2022-02-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | L5X 3-{[(5S)-5-methyl-4,5-dihydro-1,3-thiazol-2-yl]amino}phenol × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；16% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium formate
|
Resolution 1.99 Å R-free 0.230 |
| 7U3I GID4 in complex with compound 16 Deposited 2022-02-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
124–289（166 aa）
|
Not recorded | L5X 3-{[(5S)-5-methyl-4,5-dihydro-1,3-thiazol-2-yl]amino}phenol × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；16% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium formate
|
Resolution 1.99 Å R-free 0.230 |
| 7U3J GID4 in complex with compound 88 Deposited 2022-02-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | GOL GLYCEROL × 2 L6U (2S)-2-{[(2S)-2-({N-[(2,4-dimethoxyphenyl)methyl]glycyl}amino)-2-(thiophen-2-yl)acetyl]amino}-N-methyl-4-phenylbutanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；18% PEG6000, 0.1 M HEPES
|
Resolution 1.64 Å R-free 0.202 |
| 7U3K GID4 in complex with compound 89 Deposited 2022-02-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | L73 N-butylglycyl-4-tert-butyl-D-phenylalanyl-3-methoxy-N-methyl-L-phenylalaninamide × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% PEG6000, 0.1 M HEPES, 0.2 M calcium chloride
|
Resolution 2.20 Å R-free 0.313 |
| 7U3L GID4 in complex with compound 91 Deposited 2022-02-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | L4X Nalpha-{(2R,4E)-2-[(N-benzylglycyl)amino]-5-phenylpent-4-enoyl}-N,4-dimethyl-L-phenylalaninamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG3350, 0.2 M sodium fluoride
|
Resolution 2.29 Å R-free 0.249 |
| 8X7G Crystal structure of the ternary complex of GID4-PROTAC(NEP108)-BRD4(BD1). Deposited 2023-11-24 | Different construct 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
124–289（166 aa）
|
Not recorded | YAX 2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]-~{N}-[2-[2-[[2-[4-[2-(1~{H}-indol-2-ylmethylamino)ethanoylamino]cyclohexyl]-3~{H}-benzimidazol-5-yl]oxy]ethoxy]ethyl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Bis-Tris pH 6.5, 25% (v/v) polyethylene glycol 300, 30% (v/v) galactose
|
Resolution 2.70 Å R-free 0.266 |
| 8X7H Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1). Deposited 2023-11-24 | Different construct 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
124–289（166 aa）
|
Not recorded | YBI ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000
|
Resolution 2.90 Å R-free 0.301 |
| 8X7H Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1). Deposited 2023-11-24 | Different construct 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
124–289（166 aa）
|
Not recorded | YBI ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide × 1 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000
|
Resolution 2.90 Å R-free 0.301 |
| 8X7H Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1). Deposited 2023-11-24 | Different construct 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
124–289（166 aa）
|
Not recorded | YBI ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000
|
Resolution 2.90 Å R-free 0.301 |
| 8X7H Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1). Deposited 2023-11-24 | Different construct 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
124–289（166 aa）
|
Not recorded | YBI ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000
|
Resolution 2.90 Å R-free 0.301 |
| 9OK4 GID4 in complex with CLEO4-88 and ACAA1 Deposited 2025-05-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
124–289（166 aa）
Chain D
124–289（166 aa）
|
Not recorded | L6U (2S)-2-{[(2S)-2-({N-[(2,4-dimethoxyphenyl)methyl]glycyl}amino)-2-(thiophen-2-yl)acetyl]amino}-N-methyl-4-phenylbutanamide × 2 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.1 M Tris pH 7.5 and 0.2 M NaF
|
Resolution 2.28 Å R-free 0.230 |
| 9QDX GID4 in complex with Compound 1 Deposited 2025-03-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | A1I6C ~{N}'-phenylpiperidine-1-carboximidamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350
|
Resolution 2.26 Å R-free 0.296 |
| 9QDY GID4 in complex with Compound 9 Deposited 2025-03-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | A1I6B ~{N}-[3-fluoranyl-5-(5-methylfuran-2-yl)phenyl]-4-methyl-piperidine-1-carboximidamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Na HEPES pH 7.0, 15% PEG 3350
|
Resolution 2.10 Å R-free 0.254 |
| 9QDZ GID4 in complex with Compound 14 Deposited 2025-03-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | A1I6F ~{N}-[3-fluoranyl-5-(5-methyl-4-piperidin-1-ylcarbonyl-furan-2-yl)phenyl]-4,4-dimethyl-piperidine-1-carboximidamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292.15 K；0.1 M Na HEPES 7.5, 7.5% 2-propanol, 20% PEG 4000
|
Resolution 1.80 Å R-free 0.244 |
| 9QZG GID4 in complex with Compound 18 Deposited 2025-04-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | A1JCC ~{N}-[3-fluoranyl-5-[4-(4-methoxypiperidin-1-yl)carbonyl-5-methyl-furan-2-yl]phenyl]-4,4-dimethyl-piperidine-1-carboximidamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Na HEPES pH 7.0,0.1 M lithium sulfate, 22.5% PEG 4000
|
Resolution 1.90 Å R-free 0.336 |
| 9QZH GID4 in complex with Compound 33 Deposited 2025-04-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292.15 K；0.1 M Na HEPES pH 7.0,0.1 M lithium sulfate, 20% PEG 4000
|
Resolution 2.19 Å R-free 0.220 |
| 9QZH GID4 in complex with Compound 33 Deposited 2025-04-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
124–289（166 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292.15 K；0.1 M Na HEPES pH 7.0,0.1 M lithium sulfate, 20% PEG 4000
|
Resolution 2.19 Å R-free 0.220 |
| 9QZH GID4 in complex with Compound 33 Deposited 2025-04-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
124–289（166 aa）
|
Not recorded | A1JCD ~{N}-[3-fluoranyl-5-[4-[4-(methoxymethyl)piperidin-1-yl]carbonyl-5-methyl-furan-2-yl]phenyl]-4,4-dimethyl-piperidine-1-carboximidamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292.15 K；0.1 M Na HEPES pH 7.0,0.1 M lithium sulfate, 20% PEG 4000
|
Resolution 2.19 Å R-free 0.220 |
| 9QZH GID4 in complex with Compound 33 Deposited 2025-04-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
124–289（166 aa）
|
Not recorded | A1JCD ~{N}-[3-fluoranyl-5-[4-[4-(methoxymethyl)piperidin-1-yl]carbonyl-5-methyl-furan-2-yl]phenyl]-4,4-dimethyl-piperidine-1-carboximidamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292.15 K；0.1 M Na HEPES pH 7.0,0.1 M lithium sulfate, 20% PEG 4000
|
Resolution 2.19 Å R-free 0.220 |
| 9QZI GID4 in complex with Compound 21 Deposited 2025-04-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
124–289（166 aa）
|
Not recorded | A1JCE ~{N}-[3-fluoranyl-5-[4-[(3~{S})-3-[2-(2-methoxyethoxy)ethyl]piperidin-1-yl]carbonyl-5-methyl-furan-2-yl]phenyl]-4,4-dimethyl-piperidine-1-carboximidamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Na HEPES pH 7.5,0.1 M lithium sulfate, 22.5% PEG 4000
|
Resolution 2.00 Å R-free 0.253 |
30 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | GID4_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–166； UniProt 124–289 |
