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6ue6

PWWP1 domain of NSD2 in complex with MR837

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone-lysine N-methyltransferase NSD2

Homo sapiens

UniProt O96028

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 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
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 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
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 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
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 211–350 Fragment：UNP residues 211-350 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
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain E； UniProt 211–350 Fragment：UNP residues 211-350 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
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain F； UniProt 211–350 Fragment：UNP residues 211-350 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
7 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain G； UniProt 211–350 Fragment：UNP residues 211-350 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
8 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain H； UniProt 211–350 Fragment：UNP residues 211-350 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

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 6UE6 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
6XCG Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934 Deposited 2020-06-08 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 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 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
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 31 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 Author chain D； PDBConstruct 2–141； UniProt 211–350 Author chain E； PDBConstruct 2–141； UniProt 211–350 Author chain F； PDBConstruct 2–141； UniProt 211–350 Author chain G； PDBConstruct 2–141； UniProt 211–350 Author chain H； PDBConstruct 2–141； UniProt 211–350

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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P(r) Distance Distribution P(r) Distribution

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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ue6
Deposition date deposition_date2019-09-20
Structure title titlePWWP1 domain of NSD2 in complex with MR837
Keywords keywordsmethyltransferase, Structural Genomics, Structural Genomics Consortium, SGC, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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