Structure of PDB 8eik Chain B Binding Site BS01

Receptor Information
>8eik Chain B (length=438) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RGDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCR
DRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVG
TGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYE
APKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEE
SIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNP
ARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRD
ISRFLECNPVMIDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDC
LEYNRIAKLKKVQTITKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHY
TDVSNMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE
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 chain8eik Chain B Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8eik Cryo-EM structure of human DNMT3B homo-hexamer
Resolution3.19 Å
Binding residue
(original residue number in PDB)		F581 S604 E605 D627 V628 R832 S833 W834
Binding residue
(residue number reindexed from 1)		F172 S195 E196 D218 V219 R417 S418 W419
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.37: DNA (cytosine-5-)-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0009008 DNA-methyltransferase activity
Biological Process
GO:0010468 regulation of gene expression

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8eik, PDBe:8eik, PDBj:8eik
PDBsum8eik
PubMed37941146
UniProtQ9UBC3|DNM3B_HUMAN DNA (cytosine-5)-methyltransferase 3B (Gene Name=DNMT3B)

[Back to BioLiP]