Structure of PDB 4p4o Chain A Binding Site BS04

Receptor Information
>4p4o Chain A (length=306) Species: 5671 (Leishmania infantum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QEMADLNNALGEKYKVSSYHKLLKKATKPKLKAIQELTQVHGFGPRAAAA
LFDREGIFTVDELLQKADSIPSLTDQQRVGIKYFYDINEKIPMQESVLHE
NYLREKCMEVLGKDFSILICGSYRRRHPFSGDVDAILSRTLDAPPLSEPV
AATGVLGHFVEFLESLKYLEATMAQGPLKYMGMGRLPPRINTKVYKARRV
DIRLIETKSVPTAMLTFTGSKNFNVIMRQAAISKGYLLNEYGLFKLGTPE
EARALYERIGIRGKNAGEELGVPKDELEDKRVEVRSEQDVFDVLGMPYAK
PENRDP
Ligand information
Ligand IDD3T
InChIInChI=1S/C10H17N2O13P3/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(23-8)5-22-27(18,19)25-28(20,21)24-26(15,16)17/h4,7-8H,2-3,5H2,1H3,(H,18,19)(H,20,21)(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1
InChIKeyURGJWIFLBWJRMF-JGVFFNPUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CCC(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O
CACTVS 3.341CC1=CN([C@H]2CC[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2CC[C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O
CACTVS 3.341CC1=CN([CH]2CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H17 N2 O13 P3
Name2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL566812
DrugBank
ZINCZINC000013519271
PDB chain4p4o Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4p4o Structures of the Leishmania infantum polymerase beta.
Resolution2.3001 Å
Binding residue
(original residue number in PDB)		G183 S184 R187 S192 G193 D194 D196 T286 F287 K291 N294
Binding residue
(residue number reindexed from 1)		G121 S122 R125 S130 G131 D132 D134 T216 F217 K221 N224
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D271
Catalytic site (residue number reindexed from 1) D201
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0016772 transferase activity, transferring phosphorus-containing groups
GO:0034061 DNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006259 DNA metabolic process
GO:0006281 DNA repair
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0005634 nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4p4o, PDBe:4p4o, PDBj:4p4o
PDBsum4p4o
PubMed24666693
UniProtQ9U6N3

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