Structure of PDB 6x9i Chain A Binding Site BS03

Receptor Information
>6x9i Chain A (length=815) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARV
TALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIH
SKVKVIYKAPSENWAMEGGMDKTYFYQLWYDQDYARFESPPKTQPNKFKF
CVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLP
PEAFTFNIPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKK
SNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFK
AVQGRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHAR
LPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGST
VFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRF
NSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLR
CLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFA
PRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALE
ISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSD
WRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKAC
DPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGK
QGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLA
KAIGLEIKLCMLAKA
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain6x9i Chain A Residue 1701 [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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PDB6x9i Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		F1145 S1146 G1150 E1168 M1169 D1190 C1191 G1223 N1578 A1579
Binding residue
(residue number reindexed from 1)		F360 S361 G365 E383 M384 D405 C406 G438 N793 A794
Annotation score5
Binding affinityBindingDB: IC50=4000nM
Enzymatic activity
Catalytic site (original residue number in PDB) C1226 E1266 R1310 R1312
Catalytic site (residue number reindexed from 1) C441 E481 R525 R527
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:6x9i, PDBe:6x9i, PDBj:6x9i
PDBsum6x9i
PubMed34790902
UniProtP26358|DNMT1_HUMAN DNA (cytosine-5)-methyltransferase 1 (Gene Name=DNMT1)

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