Structure of PDB 5gut Chain A Binding Site BS01

Receptor Information
>5gut Chain A (length=794) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKIEENRTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKN
GQMMFHAHWFCAGTDTVLGATSDPLELFLVGECENMQLSYIHSKVKVIYK
APSENWAMEGYFFQLWYNQEYARFESPPKTQPHKFCLSCIRLAELRQKEM
PKVLEQIEEVDGRVYCSSITKNGVVYRLGDSVYLPPEAFTFNIKVASPDP
VNETLYPEHYRKYDAPEPYRIGRIKEIHCGKKKGKVNEADIKLRLYKFYR
PENTHRSYNGSYHTDINMLYWSDEEAVVNFSDVQGRCTVEYGEDLLESIQ
DYSQGGPDRFYFLEAYNSKTKNFEDPPNHARSPLPKLRTLDVFSGCGGLS
EGFHQAGISETLWAIEMWDPAAQAFRLNNPGTTVFTEDCNVLLKLVMAGE
VTNSLGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKASLVVSFL
SYCDYYRPRFFLLENVRNFVSYRRSMVLKLTLRCLVRMGYQCTFGVLQAG
QYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVS
NITRLSSGPFRTITVRDTMSDLPEIQNGASNSEIPYNGEPLSWFQRQLRG
SHYQPILRDHICKDMSPLVAARMRHIPLFPGSDWRDLPNIQVRLGDGVIA
HKLQYTFHDVKNGYSSTGALRGVCSCAEGKACDPESRQFSTLIPWCLPHT
GNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVREC
ARSQGFPDSYRFFGNILDRHRQVGNAVPPPLAKAIGLEIKLCLL
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 chain5gut Chain A 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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PDB5gut Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in DNA Methyltransferase-1.
Resolution2.099 Å
Binding residue
(original residue number in PDB)		F1148 S1149 G1153 L1154 E1171 M1172 D1193 C1194 L1250 N1580 A1581 V1582
Binding residue
(residue number reindexed from 1)		F343 S344 G348 L349 E366 M367 D388 C389 L445 N775 A776 V777
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=6.29,Kd=0.51uM
Enzymatic activity
Catalytic site (original residue number in PDB) C1229 E1269 R1313 R1315
Catalytic site (residue number reindexed from 1) C424 E464 R508 R510
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:5gut, PDBe:5gut, PDBj:5gut
PDBsum5gut
PubMed29381856
UniProtP13864|DNMT1_MOUSE DNA (cytosine-5)-methyltransferase 1 (Gene Name=Dnmt1)

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