Structure of PDB 4df8 Chain A Binding Site BS03

Receptor Information
>4df8 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 ID0L4
InChIInChI=1S/C16H24N5O12P3/c17-5-3-1-2-4-10-7-21(16-14(10)15(18)19-9-20-16)13-6-11(22)12(31-13)8-30-35(26,27)33-36(28,29)32-34(23,24)25/h7,9,11-13,22H,1,3,5-6,8,17H2,(H,26,27)(H,28,29)(H2,18,19,20)(H2,23,24,25)/t11-,12+,13+/m0/s1
InChIKeyMCSGHAFVOBYWGE-YNEHKIRRSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NCCCC#Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)c3ncnc(N)c13
OpenEye OEToolkits 1.7.6c1c(c2c(ncnc2n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N)C#CCCCN
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cc(C#CCCCN)c1c(ncnc12)N)CC3O
OpenEye OEToolkits 1.7.6c1c(c2c(ncnc2n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N)C#CCCCN
CACTVS 3.370NCCCC#Cc1cn([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)c3ncnc(N)c13
FormulaC16 H24 N5 O12 P3
Name5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine
ChEMBL
DrugBank
ZINCZINC000098207824
PDB chain4df8 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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PDB4df8 Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		R573 D610 Y611 S612 Q613 I614 E615 H639 R659 R660 K663 F667 D785
Binding residue
(residue number reindexed from 1)		R280 D317 Y318 S319 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

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Molecular Function
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Biological Process
External links
PDB RCSB:4df8, PDBe:4df8, PDBj:4df8
PDBsum4df8
PubMed22475415
UniProtP19821|DPO1_THEAQ DNA polymerase I, thermostable (Gene Name=polA)

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