Structure of PDB 6x9j Chain A Binding Site BS05

Receptor Information
>6x9j Chain A (length=842) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLAR
VTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYI
HSKVKVIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFES
PPKTQPTEDNKFKFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATK
NGILYRVGDGVYLPPEAFTFNIKLSSPVKRPRKEPVDEDLYPEHYRKYSD
YIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPENTH
KSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMG
GPNRFYFLEAYNAKSKSFEDPPNHARKLPKLRTLDVFSGCGGLSEGFHQA
GISDTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMAGETTNSRG
QRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYY
RPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQ
TRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLS
SGPFRTITVRDTMSDLPEVRNGASALEISYNGEPQSWFQRQLRGAQYQPI
LRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTMARKLRYT
HHDRKNGRSSSGALRGVCSCVEAGKACDPAARQFNTLIPWCLPHTGNRHN
HWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQG
FPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKA
Ligand information
Ligand IDX52
InChIInChI=1S/C22H28N6O2S2/c1-6-18-19(13-23)21(27(3)12-11-25-2)26-22(20(18)14-24)31-15-16-7-9-17(10-8-16)28(4)32(5,29)30/h7-10,25H,6,11-12,15H2,1-5H3
InChIKeyGQHBHKILJGTNGL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCc1c(c(nc(c1C#N)SCc2ccc(cc2)N(C)S(=O)(=O)C)N(C)CCNC)C#N
ACDLabs 12.01CCc1c(C#N)c(N(CCNC)C)nc(c1C#N)SCc2ccc(cc2)N(C)S(C)(=O)=O
CACTVS 3.385CCc1c(C#N)c(SCc2ccc(cc2)N(C)[S](C)(=O)=O)nc(N(C)CCNC)c1C#N
FormulaC22 H28 N6 O2 S2
NameN-(4-{[(3,5-dicyano-4-ethyl-6-{methyl[2-(methylamino)ethyl]amino}pyridin-2-yl)sulfanyl]methyl}phenyl)-N-methylmethanesulfonamide
ChEMBL
DrugBank
ZINC
PDB chain6x9j Chain D Residue 101 [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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PDB6x9j Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia.
Resolution1.79 Å
Binding residue
(original residue number in PDB)
Q1227 S1230 K1535
Binding residue
(residue number reindexed from 1)
Q469 S472 K777
Annotation score1
Binding affinityBindingDB: IC50=<320nM
Enzymatic activity
Catalytic site (original residue number in PDB) C1226 E1266 R1310 R1312
Catalytic site (residue number reindexed from 1) C468 E508 R552 R554
Enzyme Commision number 2.1.1.37: DNA (cytosine-5-)-methyltransferase.
Gene Ontology
Molecular Function
GO:0003682 chromatin binding
GO:0008168 methyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:6x9j, PDBe:6x9j, PDBj:6x9j
PDBsum6x9j
PubMed34790902
UniProtP26358|DNMT1_HUMAN DNA (cytosine-5)-methyltransferase 1 (Gene Name=DNMT1)

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