Structure of PDB 6kjm Chain A Binding Site BS02

Receptor Information

>6kjm Chain A (length=321) Species: 83332 (Mycobacterium tuberculosis H37Rv)

QTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQ
HPELRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGR
IHAEVGDAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNA
RTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPF
ANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLALR
AWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQ
RRLGSTSRAPRWAIAYKYPPE

Ligand information

• Ligand ID: AMP
• InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: UDMBCSSLTHHNCD-KQYNXXCUSA-N
• SMILES:
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
  ACDLabs 12.01: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
• Formula: C10 H14 N5 O7 P
• Name: ADENOSINE MONOPHOSPHATE
• ChEMBL: CHEMBL752
• DrugBank: DB00131
• ZINC: ZINC000003860156
• PDB chain: 6kjm Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6kjm Structure based identification of first-in-class fragment inhibitors that target the NMN pocket of M. tuberculosis NAD + -dependent DNA ligase A.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): E121 K123 I124 E184 H236 K300
• Binding residue (residue number reindexed from 1): E114 K116 I117 E177 H229 K293
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 6.5.1.2: DNA ligase (NAD(+)).

Gene Ontology

Molecular Function

• GO:0003911 DNA ligase (NAD+) activity

External links

• PDB: RCSB:6kjm, PDBe:6kjm, PDBj:6kjm
• PDBsum: 6kjm
• PubMed: 33197566
• UniProt: P9WNV1|DNLJ_MYCTU DNA ligase A (Gene Name=ligA)