Structure of PDB 6g0a Chain A Binding Site BS03

Receptor Information
>6g0a Chain A (length=1104) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NNYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVG
WLTNMHATLVSQETNQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDE
SRVNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNS
NQLFEARKLLRPILQDNARNIYNVDAKHLIEDIREYDVPYHVRVSIDKDI
RVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFRDSAVDQIM
MISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVALL
QRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDAE
GEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPELM
TPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETLR
KGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGHVE
SLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKVTN
FEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMTTNRLQPDSI
KAERTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKKKVLTFDEL
SYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENPFYVDTVKS
FRDRRYEFKGLAKTWKGNLSKHARDEAKKMIVLYDSLQLAHKVILNSFYG
YVMRKGSRWYSMEMAGITCLTGATIIQMARALVERVGRPLELDTDGIWCI
LPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKFTNHQYQELKDPLNY
IYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEDGSLAELK
GFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSAVASVCNRWLDVLDS
HGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSITTARRLGDFLGEDMV
KDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPIKRSFLRRWTLDPSL
EDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVSNPVPRVEHPDWLKR
KIAT
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 chain6g0a 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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PDB6g0a Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon.
Resolution2.62 Å
Binding residue
(original residue number in PDB)		S643 M644 Y645 R781 K824 N828 D877
Binding residue
(residue number reindexed from 1)		S584 M585 Y586 R705 K742 N746 D795
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:6g0a, PDBe:6g0a, PDBj:6g0a
PDBsum6g0a
PubMed30670696
UniProtP21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)

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