Structure of PDB 6q4t Chain A Binding Site BS05

Receptor Information
>6q4t Chain A (length=757) Species: 69014 (Thermococcus kodakarensis KOD1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MILDTDYITEDGKPVIRIFKKENGEFKIEYDRTFEPYFYALLKDDSAIEE
VKKITAERHGTVVTVKRVEKVQKKFLGRPVEVWKLYFTHPQDVPAIRDKI
REHPAVIDIYEYDIPFAKRYLIDKGLVPMEGDEELKMLAFAIATLYHEGE
EFAEGPILMISYADEEGARVITWKNVDLPYVDVVSTEREMIKRFLRVVKE
KDPDVLITYNGDNFDFAYLKKRCEKLGINFALGRDGSEPKIQRMGDRFAV
EVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTAWE
TGENLERVARYSMEDAKVTYELGKEFLPMEAQLSRLIGQSLWDVSRSSTG
NLVEWFLLRKAYERNELAPNKPDEKELARRRQSYEGGYVKEPERGLWENI
VYLDFRSLYPSIIITHNVSPDTLNREGCKEYDVAPQVGHRFCKDFPGFIP
SLLGDLLEERQKIKKKMKATIDPIERKLLDYRQRAIKILANSYYGYYGYA
RARWYCKECAESVTAWGREYITMTIKEIEEKYGFKVIYSDTDGFFATIPG
ADAETVKKKAMEFLKYINAKLPGALELEYEGFYKRGFFVTKKKYAVIDEE
GKITTRGLEIVRRDWSEIAKETQARVLEALLKDGDVEKAVRIVKEVTEKL
SKYEVPPEKLVIHEQITRDLKDYKATGPHVAVAKRLAARGVKIRPGTVIS
YIVLKGSGRIGDRAIPFDEFDPTKHKYDAEYYIENQVLPAVERILRAFGY
RKEDLRY
Ligand information
Ligand IDHHZ
InChIInChI=1S/C18H26N5O15P3/c19-17-16-11(2-1-3-20-14(26)9-34-5-4-24)7-23(18(16)22-10-21-17)15-6-12(25)13(36-15)8-35-40(30,31)38-41(32,33)37-39(27,28)29/h7,10,12-13,15,24-25H,3-6,8-9H2,(H,20,26)(H,30,31)(H,32,33)(H2,19,21,22)(H2,27,28,29)/t12-,13+,15+/m0/s1
InChIKeyFDFHIISDJKYZQH-GZBFAFLISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1c(c2c(ncnc2n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N)C#CCNC(=O)COCCO
CACTVS 3.385Nc1ncnc2n(cc(C#CCNC(=O)COCCO)c12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 2.0.6c1c(c2c(ncnc2n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N)C#CCNC(=O)COCCO
CACTVS 3.385Nc1ncnc2n(cc(C#CCNC(=O)COCCO)c12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
FormulaC18 H26 N5 O15 P3
Name[[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain6q4t Chain A Residue 810 [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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PDB6q4t The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide.
Resolution1.997 Å
Binding residue
(original residue number in PDB)
D404 F405 S407 L408 Y409 R460 K487 N491 D542 R606
Binding residue
(residue number reindexed from 1)
D404 F405 S407 L408 Y409 R460 K487 N491 D542 R606
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.-.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity

View graph for
Molecular Function
External links
PDB RCSB:6q4t, PDBe:6q4t, PDBj:6q4t
PDBsum6q4t
PubMed30761722
UniProtP77933|DPOL_THEKO DNA polymerase (Gene Name=pol)

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