Structure of PDB 6ajp Chain A Binding Site BS01

Receptor Information

>6ajp Chain A (length=206) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

AGAQDFVPHTADLAELAAAAGECRGCGLYRDATQAVFGAGGRSARIMMIG
EQPGDKEDLAGLPFVGPAGRLLDRALEAADIDRDALYVTNAVKHFKFTRA
AGGKRRIHKTPSRTEVVACRPWLIAEMTSVEPDVVVLLGATAAKALLGND
FRVTQHRGEVLHVDDVPGDPALVATVHPSSLLRGPKEERESAFAGLVDDL
RVAADV

Ligand information

• Ligand ID: DU
• InChI: InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
• InChIKey: JSRLJPSBLDHEIO-SHYZEUOFSA-N
• SMILES:
  CACTVS 3.341: O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  ACDLabs 10.04: O=C1NC(=O)N(C=C1)C2OC(C(O)C2)COP(=O)(O)O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
  CACTVS 3.341: O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
• Formula: C9 H13 N2 O8 P
• Name: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL211312
• DrugBank: DB03800
• ZINC: ZINC000004228260
• PDB chain: 6ajp Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ajp Covalent binding of uracil DNA glycosylase UdgX to abasic DNA upon uracil excision.
• Resolution: 1.334 Å
• Binding residue (original residue number in PDB): E52 Q53 E58 P64 F65 P68 A69 N91 H178 S180
• Binding residue (residue number reindexed from 1): E51 Q52 E57 P63 F64 P67 A68 N90 H177 S179
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0004844 uracil DNA N-glycosylase activity
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0097506 deaminated base DNA N-glycosylase activity

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:6ajp, PDBe:6ajp, PDBj:6ajp
• PDBsum: 6ajp
• PubMed: 31101917
• UniProt: A0QP43