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 homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count | Chain A； UniProt 211–350 Chain B； UniProt 211–350 Chain C； UniProt 211–350 Chain D； UniProt 211–350 Chain E； UniProt 211–350 Chain F； UniProt 211–350 Chain G； UniProt 211–350 Chain H； UniProt 211–350 | Fragment：UNP residues 211-350 | 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 |
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 7LMT | 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 oligomeric state 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 oligomeric state 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 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
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 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
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 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
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 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
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 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
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 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
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 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
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 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
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 |
| 6XCG Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934 Deposited 2020-06-08 | 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
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | 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 |
| 6XCG Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934 Deposited 2020-06-08 | 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 B
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | 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 |
| 6XCG Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934 Deposited 2020-06-08 | 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 C
211–350（140 aa）
Fragment：UNP residues 211-350
|
Not recorded | 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 |
| 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 |
| 7MDN Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a Deposited 2021-04-05 | 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 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
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 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
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 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
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 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
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 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
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 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
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 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
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 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
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 oligomeric state 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 oligomeric state 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 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
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 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
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 oligomeric state 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 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
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 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
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 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
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 38 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 1–140； UniProt 211–350 Author chain B； PDBConstruct 1–140； UniProt 211–350 Author chain C； PDBConstruct 1–140； UniProt 211–350 Author chain D； PDBConstruct 1–140； UniProt 211–350 Author chain E； PDBConstruct 1–140； UniProt 211–350 Author chain F； PDBConstruct 1–140； UniProt 211–350 Author chain G； PDBConstruct 1–140； UniProt 211–350 Author chain H； PDBConstruct 1–140； UniProt 211–350 |