Structure of PDB 8d3r Chain A Binding Site BS03

Receptor Information
>8d3r Chain A (length=958) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LRHNPLDIQMLSRGLHEQIFGQGGEMPGEAAVRRSVEHLQKHGLWGQPAV
PLPDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPA
WAWAEGWTRYGPEGEAVPVAIPEERALVFDVEVCLAEGTCPTLAVAISPS
AWYSWCSQRLVEERYSWTSQLSPADLIPLEVPTWQEQLVVGHNVSFDRAH
IREQYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKAISSWDWLDIS
SVNSLAEVHRLYVGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVW
ATHEVFQQQLPLFLERCPHPVTLAGMLEMGVSYLPVNQNWERYLAEAQGT
YEELQREMKKSLMDLANDACQLLSGERYKEDPWLWDLEWDLQEFKQKKPC
SEEEEFQQDVMARACLQKLKGTTELLPKRPQHLPGHPGWYRKLCPRLDDP
AWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLVPGRVVCPYR
AIESLYRKHCLEQYHHGNGPYNDVDIPGCWFFKLPHKDGNSCNVGSPFAK
DFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAHKRISSQMVVWLPR
SALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASNARPD
RVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGW
MTLQGRKSRGTDLHSKTATTVGISREHAKIFNYGRIYGAGQPFAERLLMQ
FNHRLTQQEAAEKAQQMYAATWKGGTESEMFNKLESIATSDIPRTPVLGC
CISRALEPSAVQEEFMTSRVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDG
RFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSV
AFFSAVDIDRCLRKEVTMDCKTPSNPTGMERRYGIPQGEALDIYQIIELT
KGSLEKRS
Ligand information
Ligand IDDCP
InChIInChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyRGWHQCVHVJXOKC-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
FormulaC9 H16 N3 O13 P3
Name2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL560403
DrugBankDB03258
ZINCZINC000008215945
PDB chain8d3r 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]
PDB8d3r Pol gamma coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity.
Resolution3.04 Å
Binding residue
(original residue number in PDB)		S893 K947 Y951 Y955 H1134
Binding residue
(residue number reindexed from 1)		S675 K729 Y733 Y737 H857
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.-
4.2.99.-
Gene Ontology
Molecular Function
GO:0002020 protease binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0005515 protein binding
GO:0008310 single-stranded DNA 3'-5' DNA exonuclease activity
GO:0008408 3'-5' exonuclease activity
GO:0016787 hydrolase activity
GO:0016829 lyase activity
GO:0051575 5'-deoxyribose-5-phosphate lyase activity
Biological Process
GO:0006259 DNA metabolic process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006264 mitochondrial DNA replication
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006287 base-excision repair, gap-filling
GO:0045004 DNA replication proofreading
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0000262 mitochondrial chromosome
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005760 gamma DNA polymerase complex
GO:0032991 protein-containing complex
GO:0042645 mitochondrial nucleoid
GO:0043231 intracellular membrane-bounded organelle

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8d3r, PDBe:8d3r, PDBj:8d3r
PDBsum8d3r
PubMed37202477
UniProtP54098|DPOG1_HUMAN DNA polymerase subunit gamma-1 (Gene Name=POLG)

[Back to BioLiP]