Structure of PDB 7sfc Chain A Binding Site BS05

Receptor Information
>7sfc 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]
RISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARV
TALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIH
SKVKVIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESP
PKTQPTEDNKFKFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKN
GILYRVGDGVYLPPEAFTFNIKLSSPVKRPRKEPVDEDLYPEHYRKYSDY
IKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPENTHK
STPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGG
PNRFYFLEAYNAKSKSFEDPPNHARSKLPKLRTLDVFSGCGGLSEGFHQA
GISDTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMAGETTNSRG
QRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYY
RPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQ
TRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLS
SGPFRTITVRDTMSDLPEVRNGASALEISYNGEPQSWFQRQLRGAQYQPI
LRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTMARKLRYT
HHDRKNGRSSSGALRGVCSCVEAGKACDPAARQFNTLIPWCLPHTGNRHN
HWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQG
FPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKA
Ligand information
Ligand IDI67
InChIInChI=1S/C25H31N7OS/c1-3-20-21(13-26)24(32-10-4-9-31(2)11-12-32)30-25(22(20)14-27)34-17-19-7-5-18(6-8-19)16-29-23(33)15-28/h5-8H,3-4,9-12,15-17,28H2,1-2H3,(H,29,33)
InChIKeyQPLFMVVUDGWTPG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCc1c(C#N)c(SCc2ccc(CNC(=O)CN)cc2)nc(N3CCCN(C)CC3)c1C#N
OpenEye OEToolkits 2.0.7CCc1c(c(nc(c1C#N)SCc2ccc(cc2)CNC(=O)CN)N3CCCN(CC3)C)C#N
ACDLabs 12.01CN1CCCN(CC1)c1nc(SCc2ccc(CNC(=O)CN)cc2)c(C#N)c(CC)c1C#N
FormulaC25 H31 N7 O S
NameN-{[4-({[3,5-dicyano-4-ethyl-6-(4-methyl-1,4-diazepan-1-yl)pyridin-2-yl]sulfanyl}methyl)phenyl]methyl}glycinamide
ChEMBL
DrugBank
ZINC
PDB chain7sfc Chain A Residue 1703 [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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PDB7sfc Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors.
Resolution1.97 Å
Binding residue
(original residue number in PDB)		A807 T808 E856 D858 F1235 N1236 Y1240 M1278
Binding residue
(residue number reindexed from 1)		A78 T79 E127 D129 F477 N478 Y482 M520
Annotation score1
Enzymatic activity
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:7sfc, PDBe:7sfc, PDBj:7sfc
PDBsum7sfc
PubMed35395178
UniProtP26358|DNMT1_HUMAN DNA (cytosine-5)-methyltransferase 1 (Gene Name=DNMT1)

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