Structure of PDB 6cst Chain A Binding Site BS06

Receptor Information
>6cst Chain A (length=446) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LLRMGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIE
NMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAV
EMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLI
IVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWP
EDKRRYFIKNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKV
CSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIIT
CTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTF
SEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRAS
TVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPN
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 chain6cst Chain A Residue 619 [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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PDB6cst 2.0 angstrom resolution crystal structure of human pol kappa reveals a new catalytic function of N-clasp in DNA replication.
Resolution2.0 Å
Binding residue
(original residue number in PDB)
K25 D107 M108 D109 A110 F111 Y112 S137 T138 Y141 R144 D198 K328
Binding residue
(residue number reindexed from 1)
K10 D92 M93 D94 A95 F96 Y97 S122 T123 Y126 R129 D183 K256
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:6cst, PDBe:6cst, PDBj:6cst
PDBsum6cst
PubMed30310122
UniProtQ9UBT6|POLK_HUMAN DNA polymerase kappa (Gene Name=POLK)

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