Structure of PDB 5t14 Chain B Binding Site BS06

Receptor Information
>5t14 Chain B (length=431) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLR
KAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAV
GSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKE
VKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKNSVVFG
TSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILP
NRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLF
SETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQE
LCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAI
AKELLKTEIDADFPHPLRLRLMGVRISSFPN
Ligand information
Ligand IDDZ4
InChIInChI=1S/C10H17N6O11P3/c11-9-8-10(13-3-12-9)16(4-14-8)7-1-5(17)6(26-7)2-25-28(18,19)15-29(20,21)27-30(22,23)24/h3-7,17H,1-2H2,(H2,11,12,13)(H2,22,23,24)(H3,15,18,19,20,21)/t5-,6+,7+/m0/s1
InChIKeyWKIPJDSLGCBQCU-RRKCRQDMSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H17 N6 O11 P3
Name2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
ChEMBL
DrugBank
ZINCZINC000032016786
PDB chain5t14 Chain B Residue 604 [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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PDB5t14 Structural basis of accurate replication beyond a bulky major benzo[a]pyrene adduct by human DNA polymerase kappa.
Resolution3.0 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)		D77 M78 D79 A80 F81 Y82 S107 T108 Y111 R114 D168 K241
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
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Biological Process
External links
PDB RCSB:5t14, PDBe:5t14, PDBj:5t14
PDBsum5t14
PubMed27894903
UniProtQ9UBT6|POLK_HUMAN DNA polymerase kappa (Gene Name=POLK)

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