Structure of PDB 8q1x Chain B Binding Site BS01

Receptor Information
>8q1x Chain B (length=419) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QRPAPCYDPCEAVLVESIPEGLDFPNAGNPSTSQAWLGLLAGAHSSLDIA
SFYWTLTNNDTHTQEPSAQQGEEVLRQLQTLAPKGVNVRIAVSKPSGPQP
QADLQALLQSGAQVRMVDMQKLTHGVLHTKFWVVDQTHFYLGSANMDWRS
LTQVKELGVVMYNCSCLARDLTKIFEAYWFLGQAGSSIPSTWPRFYDTRY
NQETPMEICLNGTPALAYLASAPPPLCPSGRTPDLKALLNVVDNARSFIY
VAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHSEPS
MRAFLLSLAALRDNHTHSDIQVKLFVVPADEAQARIPYARVNHNKYMVTE
RATYIGTSNWSGNYFTETAGTSLLVTQNGRGGLRSQLEAIFLRDWDSPYS
HDLDTSADSVGNACRLLAA
Ligand information
Ligand IDPST
InChIInChI=1S/C10H15N2O7PS/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(19-8)4-18-20(16,17)21/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,21)/t6-,7+,8+/m0/s1
InChIKeyOJRKJKYGUAALCJ-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=S)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=S)(O)O)O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=S)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=S)(O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=S)O2)C(=O)NC1=O
FormulaC10 H15 N2 O7 P S
NameTHYMIDINE-5'-THIOPHOSPHATE
ChEMBL
DrugBankDB08432
ZINC
PDB chain8q1x Chain B Residue 502 [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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PDB8q1x Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		Y126 Y411 H416
Binding residue
(residue number reindexed from 1)		Y53 Y338 H343
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.16.1: spleen exonuclease.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity

View graph for
Molecular Function
External links
PDB RCSB:8q1x, PDBe:8q1x, PDBj:8q1x
PDBsum8q1x
PubMed37994783
UniProtQ8IV08|PLD3_HUMAN 5'-3' exonuclease PLD3 (Gene Name=PLD3)

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