Structure of PDB 8d96 Chain C Binding Site BS03

Receptor Information

>8d96 Chain C (length=869) Species: 9606 (Homo sapiens)

EQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTL
YFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEK
NYAFEIPDVPEKSEYLEVKYSAEMPQLPQDLKGETFSHVFGTNTSSLELF
LMNRKIKGPCWLEVKSPQLLNQPVSWCKVEAMALKPDLVNVIKDVSPPPL
VVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFCVVS
KPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGH
NIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGFGERNATCGRMIC
DVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYL
LEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFL
LLHAFYENNYIVPDKQIAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSII
QEFNICFTTVQRVEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQ
DLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGRE
ILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKL
YKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIVRR
DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQ
FEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQD
GSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDA
VLIATWLGLDPTQFRVHHY

Ligand information

• Ligand ID: DTP
• InChI: InChI=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
• InChIKey: SUYVUBYJARFZHO-RRKCRQDMSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(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 3.341: Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
• Formula: C10 H16 N5 O12 P3
• Name: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
• ChEMBL: CHEMBL335538
• DrugBank: DB03222
• ZINC: ZINC000008215662
• PDB chain: 8d96 Chain C Residue 1501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8d96 Structures of human primosome elongation complexes.
• Resolution: 3.35 Å
• Binding residue (original residue number in PDB): S863 Y865 R922 K950
• Binding residue (residue number reindexed from 1): S494 Y496 R540 K568
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003688 DNA replication origin binding
• GO:0003697 single-stranded DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0019901 protein kinase binding
• GO:0046872 metal ion binding

Biological Process

• GO:0000731 DNA synthesis involved in DNA repair
• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006269 DNA replication, synthesis of primer
• GO:0006270 DNA replication initiation
• GO:0006271 DNA strand elongation involved in DNA replication
• GO:0006272 leading strand elongation
• GO:0006273 lagging strand elongation
• GO:0006281 DNA repair
• GO:0006289 nucleotide-excision repair
• GO:0006303 double-strand break repair via nonhomologous end joining
• GO:0032479 regulation of type I interferon production
• GO:1902975 mitotic DNA replication initiation
• GO:1904161 DNA synthesis involved in UV-damage excision repair

Cellular Component

• GO:0000785 chromatin
• GO:0005634 nucleus
• GO:0005635 nuclear envelope
• GO:0005654 nucleoplasm
• GO:0005658 alpha DNA polymerase:primase complex
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0016363 nuclear matrix
• GO:0031981 nuclear lumen

External links

• PDB: RCSB:8d96, PDBe:8d96, PDBj:8d96
• PDBsum: 8d96
• PubMed: 37069376
• UniProt: P09884|DPOLA_HUMAN DNA polymerase alpha catalytic subunit (Gene Name=POLA1)