Structure of PDB 5nkl Chain A Binding Site BS05

Receptor Information
>5nkl Chain A (length=540) 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
ASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAF
IERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVRE
AAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAP
KERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE
Ligand information
Ligand ID91T
InChIInChI=1S/C14H21N2O16P3/c17-7-10(18)3-1-2-9-4-13(16(20)21)15(6-9)14-5-11(19)12(30-14)8-29-34(25,26)32-35(27,28)31-33(22,23)24/h4,6,10-12,14,17-19H,3,5,7-8H2,(H,25,26)(H,27,28)(H2,22,23,24)/t10-,11+,12-,14-/m1/s1
InChIKeyJIVPAQSXWIKFCI-GFQSEFKGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC[C@H](O)CC#Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)c(c1)[N+]([O-])=O
CACTVS 3.385OC[CH](O)CC#Cc1cn([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)c(c1)[N+]([O-])=O
OpenEye OEToolkits 2.0.6c1c(cn(c1[N+](=O)[O-])C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)C#CCC(CO)O
OpenEye OEToolkits 2.0.6c1c(cn(c1[N+](=O)[O-])[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)C#CC[C@H](CO)O
FormulaC14 H21 N2 O16 P3
Name[[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain5nkl Chain A Residue 904 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5nkl Structural Basis for Expansion of the Genetic Alphabet with an Artificial Nucleobase Pair.
Resolution1.7 Å
Binding residue
(original residue number in PDB)
D610 Y611 Q613 I614 E615 H639 R659 R660 K663 F667 D785
Binding residue
(residue number reindexed from 1)
D318 Y319 Q321 I322 E323 H347 R367 R368 K371 F375 D493
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

View graph for
Biological Process
External links
PDB RCSB:5nkl, PDBe:5nkl, PDBj:5nkl
PDBsum5nkl
PubMed28594080
UniProtP19821|DPO1_THEAQ DNA polymerase I, thermostable (Gene Name=polA)

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