Structure of PDB 4dfk Chain A Binding Site BS03

Receptor Information
>4dfk 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 ID0L5
InChIInChI=1S/C24H40N3O16P3/c28-14-10-5-3-1-2-4-8-12-21(30)25-13-9-6-7-11-18-16-27(24(32)26-23(18)31)22-15-19(29)20(41-22)17-40-45(36,37)43-46(38,39)42-44(33,34)35/h16,19-20,22,28-29H,1-6,8-10,12-15,17H2,(H,25,30)(H,36,37)(H,38,39)(H,26,31,32)(H2,33,34,35)/t19-,20+,22+/m0/s1
InChIKeyUGHLPDROZCTFGX-TUNNFDKTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C#CCCCNC(=O)CCCCCCCCCO)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#CCCCNC(=O)CCCCCCCCCO)=C1)CC2O
CACTVS 3.370OCCCCCCCCCC(=O)NCCCC#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 3.370OCCCCCCCCCC(=O)NCCCC#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
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=C(C(=O)NC2=O)C#CCCCNC(=O)CCCCCCCCCO)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
FormulaC24 H40 N3 O16 P3
Name2'-deoxy-5-{5-[(10-hydroxydecanoyl)amino]pent-1-yn-1-yl}uridine 5'-(tetrahydrogen triphosphate)
ChEMBL
DrugBank
ZINCZINC000098207825
PDB chain4dfk Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4dfk Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates.
Resolution1.647 Å
Binding residue
(original residue number in PDB)		R587 D610 Y611 S612 Q613 I614 E615 H639 L657 R659 R660 A661 K663 T664 F667 D785
Binding residue
(residue number reindexed from 1)		R294 D317 Y318 S319 Q320 I321 E322 H346 L364 R366 R367 A368 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:4dfk, PDBe:4dfk, PDBj:4dfk
PDBsum4dfk
PubMed22475415
UniProtP19821|DPO1_THEAQ DNA polymerase I, thermostable (Gene Name=polA)

[Back to BioLiP]