PDBsum entry 5qah

Hydrolase

PDB id: 5qah

Contents

Protein chains

242 a.a.

Ligands

EFX ×4

EDO ×5

Metals

_CL ×2

Waters ×1149

PDB id:

5qah

Name:

Hydrolase

Title:

Oxa-48 in complex with compound 9b

Structure:

Beta-lactamase. Chain: a, b, c, d. Engineered: yes

Source:

Klebsiella pneumoniae. Organism_taxid: 573. Gene: bla oxa-48, blaoxa-48, kpe71t_00045. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.95Å R-factor: 0.174 R-free: 0.202

Authors:

B.A.Lund,H.K.S.Leiros

Key ref:

S.Akhter et al. (2018). A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design. Eur J Med Chem, 145, 634-648. PubMed id: 29348071 DOI: 10.1016/j.ejmech.2017.12.085

Date:

11-Jul-17 Release date: 10-Jan-18

Protein chains

Q6XEC0  (Q6XEC0_KLEPN) -  Beta-lactamase from Klebsiella pneumoniae

Seq: 265 a.a.

Struc: 242 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.5.2.6 - beta-lactamase.
• Pathway: Penicillin Biosynthesis and Metabolism
• Reaction: a beta-lactam + H2O = a substituted beta-amino acid
• Cofactor: Zn(2+)

DOI no: 10.1016/j.ejmech.2017.12.085

Eur J Med Chem 145:634-648 (2018)

PubMed id: 29348071

A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design.

S.Akhter, B.A.Lund, A.Ismael, M.Langer, J.Isaksson, T.Christopeit, H.S.Leiros, A.Bayer.

ABSTRACT

β-Lactam antibiotics are of utmost importance when treating bacterial infections in the medical community. However, currently their utility is threatened by the emergence and spread of β-lactam resistance. The most prevalent resistance mechanism to β-lactam antibiotics is expression of β-lactamase enzymes. One way to overcome resistance caused by β-lactamases, is the development of β-lactamase inhibitors and today several β-lactamase inhibitors e.g. avibactam, are approved in the clinic. Our focus is the oxacillinase-48 (OXA-48), an enzyme reported to spread rapidly across the world and commonly identified in Escherichia coli and Klebsiella pneumoniae. To guide inhibitor design, we used diversely substituted 3-aryl and 3-heteroaryl benzoic acids to probe the active site of OXA-48 for useful enzyme-inhibitor interactions. In the presented study, a focused fragment library containing 49 3-substituted benzoic acid derivatives were synthesised and biochemically characterized. Based on crystallographic data from 33 fragment-enzyme complexes, the fragments could be classified into R¹or R²binders by their overall binding conformation in relation to the binding of the R¹and R²side groups of imipenem. Moreover, binding interactions attractive for future inhibitor design were found and their usefulness explored by the rational design and evaluation of merged inhibitors from orthogonally binding fragments. The best inhibitors among the resulting 3,5-disubstituted benzoic acids showed inhibitory potential in the low micromolar range (IC₅₀ = 2.9 μM). For these inhibitors, the complex X-ray structures revealed non-covalent binding to Arg250, Arg214 and Tyr211 in the active site and the interactions observed with the mono-substituted fragments were also identified in the merged structures.