Structure of PDB 6i8a Chain A Binding Site BS03

Receptor Information
>6i8a Chain A (length=1107) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLT
NMHATLVSQENQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVN
DVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLF
EARKLLRPILQDNANNNVQRNIYNVDAKHLIEDIREYDVPYHVRVSIDKD
IRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFRDSAVDQI
MMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVAL
LQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDA
EGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPEL
MTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETL
RKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGHV
ESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKVT
NFEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMTTNRLQPDS
IKAETCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNLTFDELSY
ADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENPFYVDTVKSFR
DRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYDSLQLAHKVILN
SFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVERVGRPLELDTDG
IWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKFTNHQYQELKD
PLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEDGSL
AELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSAVASVCNRWLD
VLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSITTARRLGDFLG
EDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPIKRSFLRRWTL
DPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVSNPVPRVEHPD
WLKRKIA
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 chain6i8a Chain A Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6i8a Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon.
Resolution2.652 Å
Binding residue
(original residue number in PDB)		D640 S643 M644 Y645 R781 K824 N828 D877
Binding residue
(residue number reindexed from 1)		D582 S585 M586 Y587 R703 K746 N750 D799
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

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6i8a, PDBe:6i8a, PDBj:6i8a
PDBsum6i8a
PubMed30670696
UniProtP21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)

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