Structure of PDB 3pta Chain A Binding Site BS03

Receptor Information
>3pta Chain A (length=904) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFKRRRCGVCEVCQQPECGKCKACKDMVKFGGSGRSKQACQERRCPNMAM
KEADDDEEVDDNIPEMPSPKKMHQGKKKKQNKNRISWVGEAVKTDGKKSY
YKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHW
FCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPSENWAME
GGMDPGKTYFYQLWYDQDYARFESPPKTQPTEDNKFKFCVSCARLAEMRQ
KEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLSS
PKEPVDEDLYPEHYRKYSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIK
IRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYG
EDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSPGKLPKLRTL
DVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTEDCN
ILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSK
FKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGY
QCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLS
VVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEISYNGEP
QSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLPNI
EVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVACDPAARQFNTLI
PWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHR
VVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCM
LAKA
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 chain3pta Chain A Residue 1601 [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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PDB3pta Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		F1145 G1147 G1150 L1151 E1168 M1169 C1191 P1225 L1247 E1266 N1578 A1579 V1580
Binding residue
(residue number reindexed from 1)		F453 G455 G458 L459 E476 M477 C499 P533 L555 E574 N882 A883 V884
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) C534 E574 R618 R620
Enzyme Commision number 2.1.1.37: DNA (cytosine-5-)-methyltransferase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0008168 methyltransferase activity
GO:0008270 zinc ion binding

View graph for
Molecular Function
External links
PDB RCSB:3pta, PDBe:3pta, PDBj:3pta
PDBsum3pta
PubMed21163962
UniProtP26358|DNMT1_HUMAN DNA (cytosine-5)-methyltransferase 1 (Gene Name=DNMT1)

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