Structure of PDB 6w8w Chain B Binding Site BS03

Receptor Information
>6w8w Chain B (length=826) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DRISWLGQPMKIEENRTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLAR
VTALWEDKNGQMMFHAHWFCAGTDTVLGATSDPLELFLVGECENMQLSYI
HSKVKVIYKAPSENWAMEGGYFFQLWYNQEYARFESPPKTQPTEDNKHKF
CLSCIRLAELRQKEMPKVLEQIEEVDGRVYCSSITKNGVVYRLGDSVYLP
PEAFTFNIKVASPVKRPKKDPVNETLYPEHYRKYSDYIKGSNLDAPEPYR
IGRIKEIHCGKKKGKVNEADIKLRLYKFYRPENTHRSYNGSYHTDINMLY
WSDEEAVVNFSDVQGRCTVEYGEDLLESIQDYSQGGPDRFYFLEAYNSKT
KNFEDPPNHARSPGNIKLPKLRTLDVFSGCGGLSEGFHQAGISETLWAIE
MWDPAAQAFRLNNPGTTVFTEDCNVLLKLVMAGEVTNSLGQRLPQKGDVE
MLCGGPPCQGFSGMNRFNYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNF
VSYRRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPG
EKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTM
SDLPEIQNGASNSEIPYNGEPLSWFQRQLRGSHYQPILRDHICKDMSPLV
AARMRHIPLFPGSDWRDLPNIQVRLGDGVIAHKLQYTFHDVKNGYSSTGA
LRGVCSCAEGKACDPESRQFSTLIPWCLPHTGNRHNHWAGLYGRLEWDGF
FSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDSYRFFGNILDR
HRQVGNAVPPPLAKAIGLEIKLCLLS
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 chain6w8w Chain B 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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PDB6w8w DNMT1 activity, base flipping mechanism and genome-wide DNA methylation are regulated by the DNA sequence context
Resolution3.0 Å
Binding residue
(original residue number in PDB)		F1148 S1149 G1150 G1153 L1154 E1171 M1172 C1194 G1226 N1580 A1581 V1582
Binding residue
(residue number reindexed from 1)		F377 S378 G379 G382 L383 E400 M401 C423 G455 N806 A807 V808
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) C1229 E1269 R1313 R1315
Catalytic site (residue number reindexed from 1) C458 E495 R539 R541
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:6w8w, PDBe:6w8w, PDBj:6w8w
PDBsum6w8w
PubMed
UniProtP13864|DNMT1_MOUSE DNA (cytosine-5)-methyltransferase 1 (Gene Name=Dnmt1)

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