9knb

NSD2-PWWP1 domain bound with compound 9

Method: X-RAY DIFFRACTION D_max: 50.9 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 217–349	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

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 9KNB	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 construct 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 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 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 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 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 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 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 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 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 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 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

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 1–133； UniProt 217–349

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9knb
Deposition date deposition_date	2024-11-18
Structure title title	NSD2-PWWP1 domain bound with compound 9
Keywords keywords	PWWP, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	15.18 Å
Radius of gyration Rg (electron density) rg_electron	14.18 Å
Forward intensity I(0) i0	6666700.00
Molecular weight molecular_weight	13085.0 kDa
Excluded volume excluded_volume	12890 Å³
Envelope volume envelope_volume	19752 Å³
Hydration-shell volume shell_volume	11976 Å³
Envelope diameter envelope_diameter	49.8 Å
Shell Rg shell_rg	19.84 Å
Envelope Rg envelope_rg	14.63 Å
Shape Rg shape_rg	14.19 Å
Total Rg total_rg	15.09 Å
Total atoms total_atoms	990
Residues n_residues	125
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	50.9 Å
Rg (real space) rg_real	15.12 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	6.6670e+06
I(0) uncertainty (real space) i0_real_error	6.7950e+04
Rg (reciprocal space) rg_reciprocal	15.12 Å
I(0) (reciprocal space) i0_reciprocal	6667000.0000
Solution quality estimate total_estimate	0.7316
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.0 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.291
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1344000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.991; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase NSD2
Molecular weight formula_weight	15240.6 kDa
EC 编号 ec_number	2.1.1.357
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1080

LLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQKKSARQYHVQFFGDAPERAWIFEKSLVAFEGEGQFEKLCQESAKQAPTKAEKIKLLKPISGKLRAQWEMGIVQAEEAASMSVEERKAKFTFLYV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	N-(2-methoxyphenyl)-2-selanyl-benzamide
Molecular weight formula_weight	306.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	90

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8. Citations (1)

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Unit-cell length a length_a	55.731 Å
Unit-cell length b length_b	55.731 Å
Unit-cell length c length_c	40.448 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	3

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	1.840 Å
Low-resolution limit resolution_low	24.130 Å
R factor r_factor	0.2356
R_work r_work	0.2336
R_free r_free	0.2752

fit	/app/data/saxs_computation/kn/9knb/9knb.fit
pddf	/app/data/pr_computation/kn/9knb/9knb.pr.out
profile	/app/data/saxs_computation/kn/9knb/9knb.dat