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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：O96028 New Search
22PDB entries
39Biological assembly
56chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric（6） Consistent with all polymers
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
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 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.