Structure of PDB 4dfj Chain A Binding Site BS05

Receptor Information
>4dfj 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 ID0KL
InChIInChI=1S/C14H22N3O14P3/c15-5-3-1-2-4-9-7-17(14(20)16-13(9)19)12-6-10(18)11(29-12)8-28-33(24,25)31-34(26,27)30-32(21,22)23/h7,10-12,18H,1,3,5-6,8,15H2,(H,24,25)(H,26,27)(H,16,19,20)(H2,21,22,23)/t10-,11+,12+/m0/s1
InChIKeyWENDCSLWIXFOST-QJPTWQEYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C#CCCCN)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(C#CCCCN)=C1)CC2O
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=C(C(=O)NC2=O)C#CCCCN)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.370NCCCC#CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.370NCCCC#CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC14 H22 N3 O14 P3
Name5-(5-aminopent-1-yn-1-yl)-2'-deoxyuridine 5'-(tetrahydrogen triphosphate)
ChEMBL
DrugBank
ZINCZINC000098207820
PDB chain4dfj 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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PDB4dfj Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		D610 Y611 S612 Q613 I614 E615 H639 R659 R660 K663 T664 F667 D785
Binding residue
(residue number reindexed from 1)		D317 Y318 S319 Q320 I321 E322 H346 R366 R367 K370 T371 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:4dfj, PDBe:4dfj, PDBj:4dfj
PDBsum4dfj
PubMed22475415
UniProtP19821|DPO1_THEAQ DNA polymerase I, thermostable (Gene Name=polA)

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