Structure of PDB 8q1x Chain A Binding Site BS02

Receptor Information
>8q1x Chain A (length=420) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QRPAPCYDPCEAVLVESIPEGLDFPSTGNPSTSQAWLGLLAGAHSSLDIA
SFYWTLTNNDTHTQEPSAQQGEEVLRQLQTLAPKGVNVRIAVSKPSGPQP
QADLQALLQSGAQVRMVDMQKLTHGVLHTKFWVVDQTHFYLGSANMDWRS
LTQVKELGVVMYNCSCLARDLTKIFEAYWFLGQAGSSIPSTWPRFYDTRY
NQETPMEICLNGTPALAYLASAPPPLCPSGRTPDLKALLNVVDNARSFIY
VAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHSEPS
MRAFLLSLAALRDNHTHSDIQVKLFVVPADEAQARIPYARVNHNKYMVTE
RATYIGTSNWSGNYFTETAGTSLLVTQNGRGGLRSQLEAIFLRDWDSPYS
HDLDTSADSVGNACRLLAAQ
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 A 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)		F125 H201 K203 N218 H416 K418
Binding residue
(residue number reindexed from 1)		F52 H128 K130 N145 H343 K345
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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