Structure of PDB 6rpn Chain A Binding Site BS01

Receptor Information

>6rpn Chain A (length=232) Species: 287 (Pseudomonas aeruginosa)

GEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDEL
LLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAG
VATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHS
TDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHY
PEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNR

Ligand information

• Ligand ID: KDZ
• InChI: InChI=1S/C16H16BO5S/c18-16(19)13-8-4-7-12-9-14(17(20,21)22-15(12)13)23-10-11-5-2-1-3-6-11/h1-8,14,20-21H,9-10H2,(H,18,19)/q-1/t14-/m0/s1
• InChIKey: NCOFNSDHLWCKKT-AWEZNQCLSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: [B-]1(C(Cc2cccc(c2O1)C(=O)O)SCc3ccccc3)(O)O
  OpenEye OEToolkits 2.0.7: [B-]1([C@H](Cc2cccc(c2O1)C(=O)O)SCc3ccccc3)(O)O
  CACTVS 3.385: OC(=O)c1cccc2C[CH](SCc3ccccc3)[B-](O)(O)Oc12
  CACTVS 3.385: OC(=O)c1cccc2C[C@H](SCc3ccccc3)[B-](O)(O)Oc12
• Formula: C16 H16 B O5 S
• Name: (3~{R})-2,2-bis(oxidanyl)-3-(phenylmethylsulfanyl)-3,4-dihydro-1,2-benzoxaborinin-2-ium-8-carboxylic acid
• PDB chain: 6rpn Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6rpn Broad Spectrum beta-Lactamase Inhibition by a Thioether Substituted Bicyclic Boronate.
• Resolution: 1.409 Å
• Binding residue (original residue number in PDB): F62 Y67 W87 H114 H116 D118 H179 C198 G209 N210 H240
• Binding residue (residue number reindexed from 1): F32 Y37 W57 H84 H86 D88 H149 C168 G179 N180 H210
• Annotation score: 1
• Binding affinity: MOAD: ic50=0.2uM

Enzymatic activity

• Catalytic site (original residue number in PDB): H114 H116 D118 H179 C198 Y201 N210 H240
• Catalytic site (residue number reindexed from 1): H84 H86 D88 H149 C168 Y171 N180 H210
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

Gene Ontology

Molecular Function

• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0017001 antibiotic catabolic process

External links

• PDB: RCSB:6rpn, PDBe:6rpn, PDBj:6rpn
• PDBsum: 6rpn
• PubMed: 31841636
• UniProt: Q9K2N0