Structure of PDB 3in5 Chain A Binding Site BS03

Receptor Information
>3in5 Chain A (length=438) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQI
TSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELK
DKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKY
RAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIK
QNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPN
GQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQR
ALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEE
QYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVST
AEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPN
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain3in5 Chain A Residue 1 [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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PDB3in5 Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion
Resolution3.2 Å
Binding residue
(original residue number in PDB)		D107 M108 D109 A110 F111 Y112 S137 T138 Y141 R144 D198 K328
Binding residue
(residue number reindexed from 1)		D83 M84 D85 A86 F87 Y88 S113 T114 Y117 R120 D174 K248
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003684 damaged DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3in5, PDBe:3in5, PDBj:3in5
PDBsum3in5
PubMed19492058
UniProtQ9UBT6|POLK_HUMAN DNA polymerase kappa (Gene Name=POLK)

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