Structure of PDB 4yrg Chain A Binding Site BS02

Receptor Information

>4yrg Chain A (length=403) Species: 353153 (Trypanosoma cruzi strain CL Brener)

MVETEPVQGCRDFPPEAMRCRRHLFDVFHATAKTFGFEEYDAPVLESEEL
YIRKAGEEITEQMFNFITKGGHRVALRPEMTPSLARLLLGKGRSLLLPAK
WYSIPQCWRYERRREHYQWNMDIVGVKSVSAEVELVCAACWAMRSLGLSS
KDVGIKVNSRKVLQTVVEQAGTSDKFAPVCVIVDKMPREEVEAQLAVVDA
ITTTLSLKSIDEIAQRVGEEHEAVKELRQFFEQVEAYGYGDWVLFDASVV
RGLAYYTGIVFEGFDREGKFRALCGGGRYDNLLTTYGSPTPIPCAGFGFG
DCVIVELLQEKRLLPDIPHVVDDVVIPFDESMRPHALAVLRRLRDAGRSA
DIILDKKKVVQAFNYADRVGAVRAVLVAPEEWERGEVQVKMLRGFAVPLD
RLV

Ligand information

• Ligand ID: 4HU
• InChI: InChI=1S/C6H6BrNO/c7-6-3-1-2-5(4-9)8-6/h1-3,9H,4H2
• InChIKey: XDDGKNRSCDEWBR-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: c1cc(nc(c1)Br)CO
  CACTVS 3.385: OCc1cccc(Br)n1
  ACDLabs 12.01: c1(cccc(Br)n1)CO
• Formula: C6 H6 Br N O
• Name: (6-bromopyridin-2-yl)methanol
• ZINC: ZINC000012496091
• PDB chain: 4yrg Chain A Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4yrg A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens.
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): P125 C154 W155 R156 R165 E167 H168
• Binding residue (residue number reindexed from 1): P78 C107 W108 R109 R113 E115 H116
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=2.70,IC50>2mM

Enzymatic activity

• Enzyme Commision number: 6.1.1.21: histidine--tRNA ligase.

Gene Ontology

Molecular Function

• GO:0004821 histidine-tRNA ligase activity
• GO:0005524 ATP binding
• GO:0016874 ligase activity

Biological Process

• GO:0006427 histidyl-tRNA aminoacylation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:4yrg, PDBe:4yrg, PDBj:4yrg
• PDBsum: 4yrg
• PubMed: 26249349
• UniProt: Q4DA54