Structure of PDB 5oxj Chain A Binding Site BS05

Receptor Information
>5oxj Chain A (length=532) Species: 271 (Thermus aquaticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKAL
RDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVAR
RYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLA
HMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLER
VLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLK
STYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQ
RIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTET
ASWMDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSF
PKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERKAFN
MPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVA
RLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE
Ligand information
Ligand IDNZI
InChIInChI=1S/C12H17N2O13P3/c15-9-5-11(14-8-4-2-1-3-7(8)13-12(14)16)25-10(9)6-24-29(20,21)27-30(22,23)26-28(17,18)19/h1-4,9-11,15H,5-6H2,(H,13,16)(H,20,21)(H,22,23)(H2,17,18,19)/t9-,10+,11+/m0/s1
InChIKeyOMCWLYQAPHJDBD-HBNTYKKESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc2c(c1)NC(=O)N2[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.385O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C(=O)Nc3ccccc23
OpenEye OEToolkits 2.0.6c1ccc2c(c1)NC(=O)N2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.385O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C(=O)Nc3ccccc23
FormulaC12 H17 N2 O13 P3
Name[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain5oxj Chain A Residue 903 [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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PDB5oxj Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		D610 Y611 Q613 I614 E615 H639 R659 K663 F667 D785
Binding residue
(residue number reindexed from 1)		D318 Y319 Q321 I322 E323 H347 R359 K363 F367 D485
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0001882 nucleoside binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5oxj, PDBe:5oxj, PDBj:5oxj
PDBsum5oxj
PubMed29136072
UniProtP19821|DPO1_THEAQ DNA polymerase I, thermostable (Gene Name=polA)

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