Structure of PDB 6ibs Chain A Binding Site BS03

Receptor Information

>6ibs Chain A (length=225) Species: 573 (Klebsiella pneumoniae)

GDQRFGDLVFRQLAPNVWQHTSYLDGAVASNGLIVRDGGRVLVVDTAWTD
DQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALS
NQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNIT
VGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASM
IVMSHSAPDSRAAITHTARMADKLR

Ligand information

• Ligand ID: HB8
• InChI: InChI=1S/C13H17BNO5S/c1-13(2,3)20-12(16)15-9-6-4-5-8-7-10(14(17,18)19)21-11(8)9/h4-7,17-19H,1-3H3,(H,15,16)/q-1
• InChIKey: WAKYUFAFDTZJQR-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: CC(C)(C)OC(=O)Nc1cccc2cc(sc12)[B-](O)(O)O
  OpenEye OEToolkits 2.0.6: [B-](c1cc2cccc(c2s1)NC(=O)OC(C)(C)C)(O)(O)O
• Formula: C13 H17 B N O5 S
• Name: [7-[(2-methylpropan-2-yl)oxycarbonylamino]-1-benzothiophen-2-yl]-tris(oxidanyl)boranuide
• PDB chain: 6ibs Chain A Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ibs X-ray Crystallography Deciphers the Activity of Broad-Spectrum Boronic Acid beta-Lactamase Inhibitors.
• Resolution: 1.37 Å
• Binding residue (original residue number in PDB): L65 W93 H122 D124 H189 C208 H250
• Binding residue (residue number reindexed from 1): L24 W48 H77 D79 H144 C163 H205
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=4.96,Ki=11uM

Enzymatic activity

• Catalytic site (original residue number in PDB): H120 H122 D124 H189 C208 K211 N220 H250
• Catalytic site (residue number reindexed from 1): H75 H77 D79 H144 C163 K166 N175 H205
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

External links

• PDB: RCSB:6ibs, PDBe:6ibs, PDBj:6ibs
• PDBsum: 6ibs
• PubMed: 30996812
• UniProt: C7C422|BLAN1_KLEPN Metallo-beta-lactamase type 2 (Gene Name=blaNDM-1)