Structure of PDB 8efg Chain A Binding Site BS04

Receptor Information
>8efg Chain A (length=295) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRFKFIDIGINLTDPMFRGIYRGVQKHQDDLQDVIGRAVEIGVKKFMITG
GNLQDSKDALHLAQTNGMFFSTVGCHPTRCGEFEKNNPDLYLKELLNLAE
NNKGKVVAIGECGLDFDRLQFCPKDTQLKYFEKQFELSEQTKLPMFLHCR
NSHAEFLDIMKRNRDRCVGGVVHSFDGTKEAAAALIDLDLYIGFNGCSLK
TEANLEVLKSIPSEKLMIETDAPWCGVKSTHAGSKYIRTAFPTKKKWESG
HCLKDRNEPCHIIQILEIMSAVRDEDPLELANTLYNNTIKVFFPG
Ligand information
Ligand ID3D1
InChIInChI=1S/C10H13N5O3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(17)6(2-16)18-7/h3-7,16-17H,1-2H2,(H2,11,12,13)/t5-,6+,7+/m0/s1
InChIKeyOLXZPDWKRNYJJZ-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)CO)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO)O3
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3)CO)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO)O)N
FormulaC10 H13 N5 O3
Name(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol;
2'-DEOXYADENOSINE
ChEMBLCHEMBL449329
DrugBank
ZINCZINC000001081581
PDB chain8efg Chain A Residue 310 [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]
PDB8efg Human and bacterial TatD enzymes exhibit apurinic/apyrimidinic (AP) endonuclease activity.
Resolution1.5 Å
Binding residue
(original residue number in PDB)
T79 R80 R119 F122
Binding residue
(residue number reindexed from 1)
T78 R79 R118 F121
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.21.-
Gene Ontology
Molecular Function
GO:0004518 nuclease activity
GO:0005515 protein binding
GO:0008296 3'-5'-DNA exonuclease activity
GO:0016788 hydrolase activity, acting on ester bonds
GO:0046872 metal ion binding
Biological Process
GO:0006259 DNA metabolic process
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005739 mitochondrion

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8efg, PDBe:8efg, PDBj:8efg
PDBsum8efg
PubMed36881763
UniProtQ6P1N9|TATD1_HUMAN Deoxyribonuclease TATDN1 (Gene Name=TATDN1)

[Back to BioLiP]