Structure of PDB 4wxx Chain A Binding Site BS06

Receptor Information
>4wxx Chain A (length=1169) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKCIQCGQYLDDPDLKYGQHPPDAVDEPQMLTNEKALPQHKLTCFSVYCK
HGHLCPIDTGLIEKNIELFFSGSAKPIYDDDPSLEGGVNGKNLGPINEWW
ITGFDGGEKALIGFSTSFAEYILMDPSPEYAPIFGLMQEKIYISKIVVEF
LQSNSDSTYEDLINKIETTVPPSGLNLNRFTEDSLLRHAQFVVEQVESYD
EAGDSDEQPIFLTPCMRDLIKLAGVTLGQRRAQARRQTKATTTKLVYQIF
DTFFAEQIEKKRRRCGVCEVCQQPECGKCKACKDMVKFGGSGRSKQACQE
RRCPNMAMKEADDDEEVDDNIPEMPSPKKMQGKKKKQNKNRISWVGEAVK
TDKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQ
MFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPS
ENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKF
KFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVY
LPPEAFTFNIRKEPVDEDLYPEHYRKYLDAPEPYRIGRIKEIFCPKKSNG
RPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQ
GRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSKL
PKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTV
FTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFN
SRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRC
LVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAP
RACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEI
SYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDW
RDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACD
PAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQ
GRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAK
AIGLEIKLCMLAKALTRVW
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 chain4wxx Chain A Residue 1706 [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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PDB4wxx Crystal Structure of Human DNA Methyltransferase 1.
Resolution2.622 Å
Binding residue
(original residue number in PDB)		F1145 S1146 G1147 G1150 L1151 E1168 M1169 D1190 C1191 L1247 N1578 V1580
Binding residue
(residue number reindexed from 1)		F709 S710 G711 G714 L715 E732 M733 D754 C755 L811 N1142 V1144
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) C1226 E1266 R1310 R1312
Catalytic site (residue number reindexed from 1) C790 E830 R874 R876
Enzyme Commision number 2.1.1.37: DNA (cytosine-5-)-methyltransferase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003886 DNA (cytosine-5-)-methyltransferase activity
GO:0008168 methyltransferase activity
GO:0008270 zinc ion binding
Biological Process
GO:0006346 DNA methylation-dependent heterochromatin formation
Cellular Component
GO:0005634 nucleus

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4wxx, PDBe:4wxx, PDBj:4wxx
PDBsum4wxx
PubMed26070743
UniProtP26358|DNMT1_HUMAN DNA (cytosine-5)-methyltransferase 1 (Gene Name=DNMT1)

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