Structure of PDB 5kfm Chain A Binding Site BS04

Receptor Information
>5kfm Chain A (length=427) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGI
IAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASV
EVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLPISADLLPSTYIEGL
PQGPTVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIE
RETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKI
RSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGI
EHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKD
RNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKN
CNTSGIQTEWSPPLTMLFLCATKFSAS
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 chain5kfm Chain A Residue 505 [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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PDB5kfm Capture of a third Mg2+ is essential for catalyzing DNA synthesis.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		M14 D15 C16 F17 F18 I48 Y52 R55 R61 D115 K231
Binding residue
(residue number reindexed from 1)		M17 D18 C19 F20 F21 I51 Y55 R58 R64 D118 K226
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:5kfm, PDBe:5kfm, PDBj:5kfm
PDBsum5kfm
PubMed27284197
UniProtQ9Y253|POLH_HUMAN DNA polymerase eta (Gene Name=POLH)

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