Structure of PDB 3av6 Chain A Binding Site BS05

Receptor Information
>3av6 Chain A (length=1135) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKCPECGQHLDDPNLKYQQHPEDAVDEPQMLTSEKLSTYEDSPMHRFTSF
SVYCSRGHLCPVDTGLIEKNVELYFSGCAKAIHDENPSMEGGINGKNLGP
INQWWLSGFDGGEKVLIGFSTAFAEYILMEPSKEYEPIFGLMQEKIYISK
IVVEFLQNNPDAVYEDLINKIETTVPPSTINVNRFTEDSLLRHAQFVVSQ
VESYDEAKDDDETPIFLSPCMRALIHLAGVSLGQRRATRPTKATTTKLVY
QIFDTFFSEQIERRRCGVCEVCQQPEACLKRRCPNLAVKEADDDEEADDE
MPSPKKLHQGKKKKQNKDRISWLGQPMKIERTYYQKVSIDEEMLEVGDCV
SVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGTDTVLGATSDPLE
LFLVGECENMQLSYIHSKVKVIYKAPSENWAMEGGKTYFFQLWYNQEYAR
FESPPKTQPTEDNKHKFCLSCIRLAELRQKEMPKVLEQIEEVDGRVYCSS
ITKNGVVYRLGDSVYLPPEAFTFNIKKKDPVNETLYPEHYRKYSLDAPEP
YRIGRIKEIHCGKKKGKVNEADIKLRLYKFYRPENTHRSYNGSYHTDINM
LYWSDEEAVVNFSDVQGRCTVEYGEDLLESIQDYSQGGPDRFYFLEAYNS
KTKNFEDPPNHARSKLPKLRTLDVFSGCGGLSEGFHQAGISETLWAIEMW
DPAAQAFRLNNPGTTVFTEDCNVLLKLVMAGEVTNSLGQRLPQKGDVEML
CGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRN
FVSYRRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAP
GEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDT
MSDLPEIQNGASNSEIPYNGEPLSWFQRQLRGSHYQPILRDHICKDMSPL
VAARMRHIPLFPGSDWRDLPNIQVRLGDGVIAHKLQYTFHDVKNGYSSTG
ALRGVCSCAEGKACDPESRQFSTLIPWCLPHTGNRHNHWAGLYGRLEWDG
FFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDSYRFFGNILD
RHRQVGNAVPPPLAKAIGLEIKLCLLSSARESASA
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain3av6 Chain A Residue 1 [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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PDB3av6 Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).
Resolution3.09 Å
Binding residue
(original residue number in PDB)		F1148 G1153 E1171 M1172 D1193 C1194 G1226 N1580 A1581 V1582
Binding residue
(residue number reindexed from 1)		F675 G680 E698 M699 D720 C721 G753 N1107 A1108 V1109
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) C1229 E1269 R1313 R1315
Catalytic site (residue number reindexed from 1) C756 E796 R840 R842
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:3av6, PDBe:3av6, PDBj:3av6
PDBsum3av6
PubMed21518897
UniProtP13864|DNMT1_MOUSE DNA (cytosine-5)-methyltransferase 1 (Gene Name=Dnmt1)

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