Structure of PDB 7r0t Chain A Binding Site BS01

Receptor Information

>7r0t Chain A (length=289) Species: 1298530 (Thermus phage TSP4)

HHHHHHRQYNLVTRESLPQALRRIEEAKRIALDTETTGLQIYLPGFELVG
LAVAVSPEEAYYFPYAHRDFAGLRYQPENLSREDLLRVLELAFQRSVVYH
NAAYDRQVLYRTLGIPFERSYGNDTMIALHLMDENHSNSLKEWSKTLLGL
EESMPELPSLTDVELVDTRKYKKKVHKLAPDWLDRLKTAFLSVHNGGVSF
AALHKLVAQAFNTLKARGILYYPGSFPVDFRYFHVHLAHIYALDDAMNTL
ALWEHVEIFLQLHPQLERLYLDIELPVNDIMTRASARGV

Ligand information

• Ligand ID: TMP
• InChI: InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
• InChIKey: GYOZYWVXFNDGLU-XLPZGREQSA-N
• SMILES:
  CACTVS 3.341: CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
  CACTVS 3.341: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
  ACDLabs 10.04: O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
• Formula: C10 H15 N2 O8 P
• Name: THYMIDINE-5'-PHOSPHATE
• ChEMBL: CHEMBL394429
• DrugBank: DB01643
• ZINC: ZINC000001678872
• PDB chain: 7r0t Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7r0t Crystal structure of DNA polymerase I from Thermus phage G20c.
• Resolution: 2.194 Å
• Binding residue (original residue number in PDB): D32 E34 T35 L38 F207 Y248 D252
• Binding residue (residue number reindexed from 1): D33 E35 T36 L39 F200 Y241 D245
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0008408 3'-5' exonuclease activity

Biological Process

• GO:0006139 nucleobase-containing compound metabolic process
• GO:0006261 DNA-templated DNA replication

External links

• PDB: RCSB:7r0t, PDBe:7r0t, PDBj:7r0t
• PDBsum: 7r0t
• PubMed: 36322421
• UniProt: A0A411CW45