Structure of PDB 2iry Chain B Binding Site BS02

Receptor Information

>2iry Chain B (length=283) Species: 83332 (Mycobacterium tuberculosis H37Rv)

EQRVTLTNADKVLYPATGTTKSDIFDYYAGVAEVMLGHIAGRPATRKRWP
NGVDQPAFFEKQLALSAPPWLSRATVAHRSGTTTYPIIDSATGLAWIAQQ
AALEVHVPQWRFVAEPGSGELNPGPATRLVFDLDPGEGVMMAQLAEVARA
VRDLLADIGLVTFPVTSGSKGLHLYTPLDEPVSSRGATVLAKRVAQRLEQ
AMPALVTSTMTKSLRAGKVFVDWSQNSGSKTTIAPYSLRGRTHPTVAAPR
TWAELDDPALRQLSYDEVLTRIARDGDLLERLD

Ligand information

• Ligand ID: DGT
• InChI: InChI=1S/C10H16N5O13P3/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
• InChIKey: HAAZLUGHYHWQIW-KVQBGUIXSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[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(n2cnc1c2N=C(N)NC1=O)CC3O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
• Formula: C10 H16 N5 O13 P3
• Name: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL477486
• DrugBank: DB02181
• ZINC: ZINC000008215755
• PDB chain: 2iry Chain B Residue 1103

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2iry Structure and function of a mycobacterial NHEJ DNA repair polymerase.
• Resolution: 1.78 Å
• Binding residue (original residue number in PDB): D140 S175 S177 K178 G179 H181 R247
• Binding residue (residue number reindexed from 1): D132 S167 S169 K170 G171 H173 R239
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 6.5.1.1: DNA ligase (ATP).

External links

• PDB: RCSB:2iry, PDBe:2iry, PDBj:2iry
• PDBsum: 2iry
• PubMed: 17174332
• UniProt: P9WNV3|LIGD_MYCTU Multifunctional non-homologous end joining DNA repair protein LigD (Gene Name=ligD)