Structure of PDB 3swr Chain A Binding Site BS01

Receptor Information
>3swr Chain A (length=965) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RQTIRHSTREPTKATTTKLVYQIFDTFFAEQINAFKRRRCGVCEVCQQPE
CGKCKACKDMVKFGGSGRSKQACQERRCPNMAMKEADDDEEVDDNIPEMP
SPKKMHQGKKKKQNKNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCV
SVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLE
LFLVDECEDMQLSYIHSKVKVIYKAPSENWAMEGGMDPESLLEGDDGKTY
FYQLWYDQDYARFESPPKTQPTEDNKFKFCVSCARLAEMRQKEIPRVLEQ
LEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLSSPVKRPRKEP
VDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETD
IKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVE
YGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSPEPEIEIK
LPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGST
VFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRF
NSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLR
CLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFA
PRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALE
ISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSD
WRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKAC
DPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGK
QGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLA
KAIGLEIKLCMLAKA
Ligand information
Ligand IDSFG
InChIInChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
InChIKeyLMXOHSDXUQEUSF-YECHIGJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
CACTVS 3.370N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N7 O5
NameSINEFUNGIN;
ADENOSYL-ORNITHINE
ChEMBLCHEMBL1214186
DrugBankDB01910
ZINCZINC000004217451
PDB chain3swr Chain A Residue 300 [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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PDB3swr Structure of human DNMT1 (residues 600-1600) in complex with Sinefungin
Resolution2.49 Å
Binding residue
(original residue number in PDB)		F1145 S1146 G1150 L1151 E1168 M1169 L1247 N1578 A1579 V1580
Binding residue
(residue number reindexed from 1)		F510 S511 G515 L516 E533 M534 L612 N943 A944 V945
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) C1226 E1266 R1310 R1312
Catalytic site (residue number reindexed from 1) C591 E631 R675 R677
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
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Biological Process
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Cellular Component
External links
PDB RCSB:3swr, PDBe:3swr, PDBj:3swr
PDBsum3swr
PubMed
UniProtP26358|DNMT1_HUMAN DNA (cytosine-5)-methyltransferase 1 (Gene Name=DNMT1)

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