Structure of PDB 6fwk Chain B Binding Site BS05

Receptor Information
>6fwk Chain B (length=1099) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWL
TNMHATLVSQENQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRV
NDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQL
FEARKLLRPILQDNANNNVQRNIYNVVDAKHLIEDIREYDVPYHVRVSID
KDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAVD
QIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEV
ALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAP
DAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDP
ELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDE
TLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGG
HVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDK
VTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASGYPNIMTTNRLQP
DSIKTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNLTFDELSYAD
QVIHIKKRLTEYSRKVSEIVEREAIVCQRENPFYVDTVKSFRDRRYEFKG
LAKTWKGNLSKIDPSDKHARDEAKKMIVLYDSLQLAHKVILNSFYGYVMR
KGSRWYSMEMAGITCLTGATIIQMARALVERVGRPLELDTDGIWCILPKS
FPETYFFTLENGKKLYLSYPCSMLNYRVHQKFTNHQYQELKDPLNYIYET
HSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEDGSLAELKGFEL
KRRGELQLIKNFQSDIFKVFLEGDTLEGCYSAVASVCNRWLDVLDSHGLM
LEDEDLVSLICENRSMSKTLKEYEGQKSTSITTARRLGDFLGEDMVKDKG
LQCKYIISSKPFNAPVTERAIPVAIFSADIPIKRSFLRRWTLDPSLEDLD
IRTIIDWGYYRERLGSAIQKIITIPAALQGVSNPVPRVEHPDWLKRKIA
Ligand information
Ligand IDDTP
InChIInChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
InChIKeySUYVUBYJARFZHO-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
FormulaC10 H16 N5 O12 P3
Name2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL335538
DrugBankDB03222
ZINCZINC000008215662
PDB chain6fwk Chain B Residue 1301 [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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PDB6fwk Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon.
Resolution2.503 Å
Binding residue
(original residue number in PDB)		V641 A642 S643 G644 Y645 R781 K824 N828 D877
Binding residue
(residue number reindexed from 1)		V585 A586 S587 G588 Y589 R695 K738 N742 D791
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006260 DNA replication
GO:0006281 DNA repair
Cellular Component
GO:0008622 epsilon DNA polymerase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6fwk, PDBe:6fwk, PDBj:6fwk
PDBsum6fwk
PubMed30670696
UniProtP21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)

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