Structure of PDB 6kqp Chain A Binding Site BS01

Receptor Information
>6kqp Chain A (length=220) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKKPPPYKHIKVNRPIGRVQIFTADLSEIPRCNCKATDENPCGIDSECIN
RMLLYECHPTVCPAGGRCQNQCFSKRQYPEVEIFRTLQRGWGLRTKTDIK
KGEFVNEYVGELIDEEECRARIRYAQEHDITNFYMLTLDKDRIIDAGPKG
NYARFMNHCCQPNCETQKWSVNGDTRVGLFALSDIKAGTELTFNYNLECL
GNGKTVCKCGAPNCSGFLGV
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain6kqp Chain A Residue 2101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6kqp Covalent inhibition of NSD1 histone methyltransferase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R1952 W1954 T1994 N1995 F1996 Y1997 R2017 N2020 H2021 Y2058 N2065 C2070 K2071 L2081
Binding residue
(residue number reindexed from 1)		R89 W91 T131 N132 F133 Y134 R154 N157 H158 Y195 N202 C207 K208 L218
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.357: [histone H3]-lysine(36) N-dimethyltransferase.
Gene Ontology
Molecular Function
GO:0042054 histone methyltransferase activity
Cellular Component
GO:0005634 nucleus

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:6kqp, PDBe:6kqp, PDBj:6kqp
PDBsum6kqp
PubMed32868895
UniProtQ96L73|NSD1_HUMAN Histone-lysine N-methyltransferase, H3 lysine-36 specific (Gene Name=NSD1)

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