Structure of PDB 4elt Chain A Binding Site BS03

Receptor Information
>4elt Chain A (length=539) Species: 271 (Thermus aquaticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALR
DLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARR
YGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAH
MEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERV
LFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKS
TYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQR
IRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETA
SWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFI
ERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREA
AERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPK
ERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE
Ligand information
Ligand ID0R5
InChIInChI=1S/C19H19N2O14P3/c1-2-12-3-5-13(6-4-12)7-8-14-10-21(19(24)20-18(14)23)17-9-15(22)16(33-17)11-32-37(28,29)35-38(30,31)34-36(25,26)27/h1,3-6,10,15-17,22H,9,11H2,(H,28,29)(H,30,31)(H,20,23,24)(H2,25,26,27)/t15-,16+,17+/m0/s1
InChIKeyNDHYKBWELLKQHS-GVDBMIGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=C(C#Cc3ccc(cc3)C#C)C(=O)NC2=O
OpenEye OEToolkits 1.7.6C#Cc1ccc(cc1)C#CC2=CN(C(=O)NC2=O)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(N2C(=O)NC(=O)C(C#Cc1ccc(C#C)cc1)=C2)CC3O
OpenEye OEToolkits 1.7.6C#Cc1ccc(cc1)C#CC2=CN(C(=O)NC2=O)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=C(C#Cc3ccc(cc3)C#C)C(=O)NC2=O
FormulaC19 H19 N2 O14 P3
Name2'-deoxy-5-[(4-ethynylphenyl)ethynyl]uridine 5'-(tetrahydrogen triphosphate)
ChEMBL
DrugBank
ZINCZINC000098207851
PDB chain4elt Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4elt Interactions of non-polar and "Click-able" nucleotides in the confines of a DNA polymerase active site.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R573 R587 D610 Y611 Q613 I614 E615 H639 R659 R660 K663 F667 D785
Binding residue
(residue number reindexed from 1)		R280 R294 D317 Y318 Q320 I321 E322 H346 R366 R367 K370 F374 D492
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:4elt, PDBe:4elt, PDBj:4elt
PDBsum4elt
PubMed22766607
UniProtP19821|DPO1_THEAQ DNA polymerase I, thermostable (Gene Name=polA)

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