Histone-lysine N-methyltransferase NSD2
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 211–350 | Fragment：UNP residues 211-350 | V01 N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1.6 M ammonium sulfate, 0.01 M magnesium chloride, 0.1 M HEPES, pH 7.5 | Resolution 1.64 Å R-free 0.222 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 211–350 | Fragment：UNP residues 211-350 | V01 N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide × 1 UNX UNKNOWN LIGAND × 3 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1.6 M ammonium sulfate, 0.01 M magnesium chloride, 0.1 M HEPES, pH 7.5 | Resolution 1.64 Å R-free 0.222 |
| 3 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain C； UniProt 211–350 | Fragment：UNP residues 211-350 | V01 N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide × 1 UNX UNKNOWN LIGAND × 3 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1.6 M ammonium sulfate, 0.01 M magnesium chloride, 0.1 M HEPES, pH 7.5 | Resolution 1.64 Å R-free 0.222 |
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 6XCG | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 29HG Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10088 Deposited 2026-03-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
1–1365（1365 aa）
|
Not recorded | A1J20 ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 29HH Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2, UNC10088 and Bach1 Deposited 2026-03-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain B
1–1365（1365 aa）
|
Not recorded | A1J20 ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 29HI Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10415667 Deposited 2026-03-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
1–1365（1365 aa）
|
Not recorded | A1J21 4-[[cyclopropyl-[(~{Z})-2-methyl-4-(5-oxidanylidene-2~{H}-1,4-oxazin-3-yl)but-3-enoyl]amino]methyl]-~{N}-[3-[2-[[4-(hydroxymethyl)phenyl]carbonyl-methyl-amino]ethyl]phenyl]benzamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.90 Å |
| 5LSU Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05 | 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
973–1203（231 aa）
|
Mutation：Q975L,A978L,D1071L,G1072Q,K1073R | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；16.0%w/v PEG 3350, 0.1M NH4Cl
|
Resolution 2.14 Å R-free 0.238 |
| 5LSU Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
973–1203（231 aa）
|
Mutation：Q975L,A978L,D1071L,G1072Q,K1073R | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；16.0%w/v PEG 3350, 0.1M NH4Cl
|
Resolution 2.14 Å R-free 0.238 |
| 5VC8 Crystal structure of the WHSC1 PWWP1 domain Deposited 2017-03-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric |
Chain A
211–350（140 aa）
Chain B
211–350（140 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 39 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.1M sodium iodide,0.1M magnesium nitrate, 25%PEG3350
|
Resolution 1.80 Å R-free 0.229 |
| 6UE6 PWWP1 domain of NSD2 in complex with MR837 Deposited 2019-09-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | Q5D 4-cyano-N-cyclopropyl-N-[(thiophen-2-yl)methyl]benzamide × 1 UNX UNKNOWN LIGAND × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M potassium thiocyanate
|
Resolution 2.40 Å R-free 0.252 |
| 6UE6 PWWP1 domain of NSD2 in complex with MR837 Deposited 2019-09-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | Q5D 4-cyano-N-cyclopropyl-N-[(thiophen-2-yl)methyl]benzamide × 1 UNX UNKNOWN LIGAND × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M potassium thiocyanate
|
Resolution 2.40 Å R-free 0.252 |
| 6UE6 PWWP1 domain of NSD2 in complex with MR837 Deposited 2019-09-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | Q5D 4-cyano-N-cyclopropyl-N-[(thiophen-2-yl)methyl]benzamide × 1 UNX UNKNOWN LIGAND × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M potassium thiocyanate
|
Resolution 2.40 Å R-free 0.252 |
| 6UE6 PWWP1 domain of NSD2 in complex with MR837 Deposited 2019-09-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | Q5D 4-cyano-N-cyclopropyl-N-[(thiophen-2-yl)methyl]benzamide × 1 UNX UNKNOWN LIGAND × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M potassium thiocyanate
|
Resolution 2.40 Å R-free 0.252 |
| 6UE6 PWWP1 domain of NSD2 in complex with MR837 Deposited 2019-09-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | Q5D 4-cyano-N-cyclopropyl-N-[(thiophen-2-yl)methyl]benzamide × 1 UNX UNKNOWN LIGAND × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M potassium thiocyanate
|
Resolution 2.40 Å R-free 0.252 |
| 6UE6 PWWP1 domain of NSD2 in complex with MR837 Deposited 2019-09-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | Q5D 4-cyano-N-cyclopropyl-N-[(thiophen-2-yl)methyl]benzamide × 1 UNX UNKNOWN LIGAND × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M potassium thiocyanate
|
Resolution 2.40 Å R-free 0.252 |
| 6UE6 PWWP1 domain of NSD2 in complex with MR837 Deposited 2019-09-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain G
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | Q5D 4-cyano-N-cyclopropyl-N-[(thiophen-2-yl)methyl]benzamide × 1 UNX UNKNOWN LIGAND × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M potassium thiocyanate
|
Resolution 2.40 Å R-free 0.252 |
| 6UE6 PWWP1 domain of NSD2 in complex with MR837 Deposited 2019-09-20 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain H
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | Q5D 4-cyano-N-cyclopropyl-N-[(thiophen-2-yl)methyl]benzamide × 1 UNX UNKNOWN LIGAND × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M potassium thiocyanate
|
Resolution 2.40 Å R-free 0.252 |
| 7CRO NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP Deposited 2020-08-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain I
661–1365（705 aa）
|
Mutation：E1099K, T1150A | SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
|
Resolution 3.75 Å |
| 7E8D NSD2 E1099K mutant bound to nucleosome Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain K
973–1226（254 aa）
|
Mutation：E1099K | ZN ZINC ION × 3 SFG SINEFUNGIN × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7LMT Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a Deposited 2021-02-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric |
Chain A
211–350（140 aa）
Fragment：UNP residues 211-350
Chain B
211–350（140 aa）
Fragment：UNP residues 211-350
Chain C
211–350（140 aa）
Fragment：UNP residues 211-350
Chain D
211–350（140 aa）
Fragment：UNP residues 211-350
Chain E
211–350（140 aa）
Fragment：UNP residues 211-350
Chain F
211–350（140 aa）
Fragment：UNP residues 211-350
Chain G
211–350（140 aa）
Fragment：UNP residues 211-350
Chain H
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | Y6V ~{N}-cyclopropyl-3-oxidanylidene-~{N}-(thiophen-2-ylmethyl)-4~{H}-1,4-benzoxazine-7-carboxamide × 8 UNX UNKNOWN LIGAND × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG3350, 0.2 M magnesium chloride, 0.1M HEPES, pH 7.5
|
Resolution 2.27 Å R-free 0.260 |
| 7MDN Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a Deposited 2021-04-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric |
Chain A
211–350（140 aa）
Fragment：UNP residues 211-350
Chain B
211–350（140 aa）
Fragment：UNP residues 211-350
Chain C
211–350（140 aa）
Fragment：UNP residues 211-350
Chain D
211–350（140 aa）
Fragment：UNP residues 211-350
Chain E
211–350（140 aa）
Fragment：UNP residues 211-350
Chain F
211–350（140 aa）
Fragment：UNP residues 211-350
Chain G
211–350（140 aa）
Fragment：UNP residues 211-350
Chain H
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | Y6V ~{N}-cyclopropyl-3-oxidanylidene-~{N}-(thiophen-2-ylmethyl)-4~{H}-1,4-benzoxazine-7-carboxamide × 8 UNX UNKNOWN LIGAND × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG3350, 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5
|
Resolution 2.42 Å R-free 0.251 |
| 7VLN NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound Deposited 2021-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
217–348（132 aa）
Fragment：PWWP1 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；1.6 M ammonium sulfate, 0.01 M magnesium chloride, 0.1 M HEPES, pH 7.5
|
Resolution 3.09 Å R-free 0.345 |
| 7VLN NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound Deposited 2021-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
217–348（132 aa）
Fragment：PWWP1 domain
|
Not recorded | 7QC 4-[5-[4-(aminomethyl)-2,6-dimethoxy-phenyl]-3-methyl-imidazol-4-yl]benzenecarbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；1.6 M ammonium sulfate, 0.01 M magnesium chloride, 0.1 M HEPES, pH 7.5
|
Resolution 3.09 Å R-free 0.345 |
| 7VLN NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound Deposited 2021-10-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
217–348（132 aa）
Fragment：PWWP1 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；1.6 M ammonium sulfate, 0.01 M magnesium chloride, 0.1 M HEPES, pH 7.5
|
Resolution 3.09 Å R-free 0.345 |
| 9CVD SET Domain of Histone-Lysine N-Methyltransferase NSD2 in Complex with Selective Inhibitor Deposited 2024-07-29 | Different construct 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
984–1203（220 aa）
|
Not recorded | ZN ZINC ION × 3 A1A0M 9-{[(2M)-5-[(3R)-3-amino-3-(pyridin-2-yl)piperidin-1-yl]-2-(3,4-difluorophenyl)pyridin-4-yl]methyl}-9H-purin-6-amine × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7.5；303.15 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition
200 uM [U-2H; U-13C; U-15N; CH3 ILV] NSD2 SET domain, 50 mM TRIS, 150 mM sodium chloride, 1 mM TCEP, 1 mM 17596, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
200 uM [U-13C; U-15N] NSD2 SET domain, 50 mM TRIS, 150 mM sodium chloride, 1 mM TCEP, 1 mM 17596, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 9EXW Crystal structure of the PWWP1 domain of NSD2 bound by compound 17. Deposited 2024-04-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
208–368（161 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 2 A1H7X 7-[3-methyl-5-[2-methyl-5-[(pyridin-3-ylamino)methyl]phenyl]imidazol-4-yl]-4~{H}-1,4-benzoxazin-3-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20 % ethanol.
|
Resolution 2.43 Å R-free 0.284 |
| 9EXW Crystal structure of the PWWP1 domain of NSD2 bound by compound 17. Deposited 2024-04-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
208–368（161 aa）
|
Not recorded | A1H7X 7-[3-methyl-5-[2-methyl-5-[(pyridin-3-ylamino)methyl]phenyl]imidazol-4-yl]-4~{H}-1,4-benzoxazin-3-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20 % ethanol.
|
Resolution 2.43 Å R-free 0.284 |
| 9EXX Crystal structure of the PWWP1 domain of NSD2 bound by compound 18. Deposited 2024-04-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
208–368（161 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 EOH ETHANOL × 1 A1H7Y 4-methyl-3-[1-methyl-5-(3-oxidanylidene-4~{H}-1,4-benzoxazin-7-yl)imidazol-4-yl]-~{N}-phenyl-benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30 % ethanol
|
Resolution 1.94 Å R-free 0.265 |
| 9EXX Crystal structure of the PWWP1 domain of NSD2 bound by compound 18. Deposited 2024-04-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
208–368（161 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 3 EOH ETHANOL × 2 A1H7Y 4-methyl-3-[1-methyl-5-(3-oxidanylidene-4~{H}-1,4-benzoxazin-7-yl)imidazol-4-yl]-~{N}-phenyl-benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30 % ethanol
|
Resolution 1.94 Å R-free 0.265 |
| 9EXY Crystal structure of the PWWP1 domain of NSD2 bound by compound 34. Deposited 2024-04-09 | 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
208–368（161 aa）
|
Mutation：K256A, K257A, K304A, K312A | A1H7Z 7-[5-methyl-3-[2-methyl-5-(piperidin-1-ylmethyl)phenyl]-1,2-oxazol-4-yl]-4~{H}-1,4-benzoxazin-3-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus screen, condition G9
|
Resolution 1.70 Å R-free 0.248 |
| 9EXY Crystal structure of the PWWP1 domain of NSD2 bound by compound 34. Deposited 2024-04-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
208–368（161 aa）
|
Mutation：K256A, K257A, K304A, K312A | A1H7Z 7-[5-methyl-3-[2-methyl-5-(piperidin-1-ylmethyl)phenyl]-1,2-oxazol-4-yl]-4~{H}-1,4-benzoxazin-3-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus screen, condition G9
|
Resolution 1.70 Å R-free 0.248 |
| 9FOC Crystal structure of the PWWP1 domain of NSD2 bound by compound 11. Deposited 2024-06-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
208–368（161 aa）
|
Not recorded | A1IFS (2S)-1-[4-[[(3R)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide × 1 A1IEG (2S)-1-[4-[[(3S)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus, G1. Molecular Dimensions catalogue no.: MD1-47.
|
Resolution 1.62 Å R-free 0.255 |
| 9FOC Crystal structure of the PWWP1 domain of NSD2 bound by compound 11. Deposited 2024-06-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
208–368（161 aa）
|
Not recorded | A1IFS (2S)-1-[4-[[(3R)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide × 1 A1IEG (2S)-1-[4-[[(3S)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus, G1. Molecular Dimensions catalogue no.: MD1-47.
|
Resolution 1.62 Å R-free 0.255 |
| 9FOE Crystal structure of the PWWP1 domain of NSD2 bound by compound 7. Deposited 2024-06-11 | 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
208–368（161 aa）
|
Mutation：K256A, K257A, K304A, K312A, D351A, E285A, E291A | A1IEF 1-[[(2~{S})-1-[4-[ethyl(pyridin-4-ylmethyl)amino]-6-methyl-pyrimidin-2-yl]pyrrolidin-2-yl]methyl]urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；3.5 M sodium formate
|
Resolution 1.96 Å R-free 0.235 |
| 9GBF X-RAY structure of PHDvC5HCH tandem domain of NSD2 Deposited 2024-07-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1229–1331（103 aa）
|
Not recorded | ZN ZINC ION × 4 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；28% PEG Smear Medium, 0.1M HEPES, pH 7.5, 0.05M magnesium sulfate
|
Resolution 1.76 Å R-free 0.228 |
| 9GBF X-RAY structure of PHDvC5HCH tandem domain of NSD2 Deposited 2024-07-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1229–1331（103 aa）
|
Not recorded | ZN ZINC ION × 4 NA SODIUM ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；28% PEG Smear Medium, 0.1M HEPES, pH 7.5, 0.05M magnesium sulfate
|
Resolution 1.76 Å R-free 0.228 |
| 9KN9 NSD2-PWWP1 domain bound with compound 1. Deposited 2024-11-18 | 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
217–349（133 aa）
Chain B
217–349（133 aa）
|
Not recorded | SO4 SULFATE ION × 3 A1EF6 (Z)-N-methyl-3-sulfanyl-prop-2-enamide × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；2.5 M ammonium sulfate, 0.01 M magnesium chloride, 0.1 M HEPES (pH 7.0), and 40% (v/v) tert-butanol
|
Resolution 2.00 Å R-free 0.275 |
| 9KNA NSD2-PWWP1 domain bound with compound 6 Deposited 2024-11-18 | 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
217–348（132 aa）
Chain B
217–348（132 aa）
|
Not recorded | 6Y3 ~{N}-(4-aminophenyl)-2-selanyl-benzamide × 2 SO4 SULFATE ION × 6 GOL GLYCEROL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；292 K；0.2 M lithium sulfate, 0.1 M BIS-TRIS (pH 5.5), and 20% (m/v) PEG3350
|
Resolution 2.92 Å R-free 0.289 |
| 9KNB NSD2-PWWP1 domain bound with compound 9 Deposited 2024-11-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
217–349（133 aa）
|
Not recorded | EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 A1EF7 N-(2-methoxyphenyl)-2-selanyl-benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；292 K；0.2 M sodium formate and 20% (m/v) PEG3350
|
Resolution 1.84 Å R-free 0.275 |
21 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | NSD2_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 2–141； UniProt 211–350 Author chain B； PDBConstruct 2–141； UniProt 211–350 Author chain C； PDBConstruct 2–141； UniProt 211–350 |