Structure of PDB 8tdr Chain A Binding Site BS01

Receptor Information
>8tdr Chain A (length=273) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSAEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRYIASEVCEDSITVGMV
RHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYE
GTGRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLES
NPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTVNDKLELQECLEHGRIA
KFSKVRTHFPVFMNEKEDILWCTEMERVFGFPVHYTDVSNMSRLARQRLL
GRSWSVPVIRHLFAPLKEYFACV
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 chain8tdr Chain A Residue 1001 [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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PDB8tdr Crystal structure of the homo-tetrameric DNMT3A methyltransferase domain
Resolution3.32 Å
Binding residue
(original residue number in PDB)		F640 D641 G642 T645 E664 V665 D686 V687 G707 R891 S892 W893
Binding residue
(residue number reindexed from 1)		F15 D16 G17 T20 E39 V40 D61 V62 G82 R252 S253 W254
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.-
2.1.1.37: DNA (cytosine-5-)-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:8tdr, PDBe:8tdr, PDBj:8tdr
PDBsum8tdr
PubMed38600075
UniProtQ9Y6K1|DNM3A_HUMAN DNA (cytosine-5)-methyltransferase 3A (Gene Name=DNMT3A)

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