Structure of PDB 5kfo Chain A Binding Site BS06

Receptor Information
>5kfo Chain A (length=428) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGI
IAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASV
EVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYI
EGLPQGVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAI
ERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRK
IRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRG
IEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTK
DRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIK
NCNTSGIQTEWSPPLTMLFLCATKFSAS
Ligand information
Ligand IDSTP
InChIInChI=1S/C10H16N5O11P3S/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(24-7)2-23-29(22,30)26-28(20,21)25-27(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,30)(H2,11,12,13)(H2,17,18,19)/t5?,6?,7?,29-/m1/s1
InChIKeyCCPIKNHZOWQALM-XZPDCLKESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=S)(O)OP(=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)C3CC(O)C(CO[P](O)(=S)O[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.341Nc1ncnc2n(cnc12)C3CC(O)C(CO[P@@](O)(=S)O[P@@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=S)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@H]([C@@H](O3)CO[P@](=S)(O)O[P@](=O)(O)OP(=O)(O)O)O)N
FormulaC10 H16 N5 O11 P3 S
Name2'-DEOXYADENOSINE 5'-O-(1-THIOTRIPHOSPHATE)
ChEMBL
DrugBank
ZINC
PDB chain5kfo Chain A Residue 506 [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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PDB5kfo Capture of a third Mg2+ is essential for catalyzing DNA synthesis.
Resolution1.52 Å
Binding residue
(original residue number in PDB)		D13 M14 D15 C16 F17 F18 Y52 R55 R61 D115 K231
Binding residue
(residue number reindexed from 1)		D16 M17 D18 C19 F20 F21 Y55 R58 R64 D118 K227
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003684 damaged DNA binding
Biological Process
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5kfo, PDBe:5kfo, PDBj:5kfo
PDBsum5kfo
PubMed27284197
UniProtQ9Y253|POLH_HUMAN DNA polymerase eta (Gene Name=POLH)

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