Structure of PDB 2ido Chain A Binding Site BS02

Receptor Information

>2ido Chain A (length=172) Species: 562 (Escherichia coli)

TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPD
RLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIG
FMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEID
NSLHGALLDAQILAEVYLAMTG

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: 2ido Chain A Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ido Structure of the Escherichia coli DNA polymerase III epsilon-HOT proofreading complex.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): D12 E14 T15 M18 V65 F102
• Binding residue (residue number reindexed from 1): D7 E9 T10 M13 V60 F97
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D12 E14 E61 H162 D167
• Catalytic site (residue number reindexed from 1): D7 E9 E56 H154 D159
• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity

Biological Process

• GO:0006260 DNA replication

External links

• PDB: RCSB:2ido, PDBe:2ido, PDBj:2ido
• PDBsum: 2ido
• PubMed: 16973612
• UniProt: P03007|DPO3E_ECOLI DNA polymerase III subunit epsilon (Gene Name=dnaQ)