Structure of PDB 6pa7 Chain K Binding Site BS02

Receptor Information
>6pa7 Chain K (length=288) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HDQEFDPPKVYPPVPAEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRYIA
SEVCEDSITVGMVRHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCND
LSIVNPARKGLYEGTGRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMG
VSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTVNDK
LELQECLEHGRIAKFSKVRTDQHFPVFMNEKEDILWCTEMERVFGFPVHY
TDVSNMSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV
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 chain6pa7 Chain K Residue 1001 [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]
PDB6pa7 Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B.
Resolution2.94 Å
Binding residue
(original residue number in PDB)		F640 D641 E664 V665 D686 V687 L730 R891 W893
Binding residue
(residue number reindexed from 1)		F28 D29 E52 V53 D74 V75 L118 R267 W269
Annotation score5
Binding affinityBindingDB: IC50=>50000nM
Enzymatic activity
Enzyme Commision number 2.1.1.-
2.1.1.37: DNA (cytosine-5-)-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
Biological Process
GO:0010468 regulation of gene expression

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6pa7, PDBe:6pa7, PDBj:6pa7
PDBsum6pa7
PubMed32968275
UniProtQ9Y6K1|DNM3A_HUMAN DNA (cytosine-5)-methyltransferase 3A (Gene Name=DNMT3A)

[Back to BioLiP]