Structure of PDB 7r3y Chain A Binding Site BS03

Receptor Information
>7r3y Chain A (length=1105) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLT
NMHATLVSQEQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVND
VEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLFE
ARKLLRPILQDNANNNVQRNIYNVVDAKHLIEDIREYDVPYHVRVSIDKD
IRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAVDQI
MMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVAL
LQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDA
EGEYKSSYCSHMDCFRWLKRDSYLPQGSQGLKAVTQSKLGYNPIELDPEL
MTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETL
RKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGHV
ESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKVT
NFEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMTTNRLQPDS
IKATCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNLTFDELSYADQ
VIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENPFYVDTVKSFRDRR
YEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYDSLQLAHKVILNSFY
GYVMRKGSRWYSMEMAGITCLTGATIIQMARALVERVGRPLELDTDGIWC
ILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKFTNHQYQELKDPLN
YIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEDGSLAEL
KGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSAVASVCNRWLDVLD
SHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSITTARRLGDFLGEDM
VKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPIKRSFLRRWTLDPS
LEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVSNPVPRVEHPDWLK
RKIAT
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 chain7r3y Chain A Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7r3y Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ε variants at low dNTP levels.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		D640 V641 A642 S643 M644 Y645 R781 K824 N828 D877
Binding residue
(residue number reindexed from 1)		D582 V583 A584 S585 M586 Y587 R700 K743 N747 D796
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:7r3y, PDBe:7r3y, PDBj:7r3y
PDBsum7r3y
PubMed35822874
UniProtP21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)

[Back to BioLiP]