5DTK | pdb_00005dtk

Fragments bound to the OXA-48 beta-lactamase: Compound 17

• PDB DOI: https://doi.org/10.2210/pdb5DTK/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-18 Released: 2016-05-25 
• Deposition Author(s): Lund, B.A., Christopeit, T., Leiros, H.-K.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.172 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

Screening and Design of Inhibitor Scaffolds for the Antibiotic Resistance Oxacillinase-48 (OXA-48) through Surface Plasmon Resonance Screening.

Lund, B.A., Christopeit, T., Guttormsen, Y., Bayer, A., Leiros, H.K.

(2016) J Med Chem 59: 5542-5554

• PubMed: 27165692 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b00660
• Primary Citation Related Structures: 
  5DTK, 5DTS, 5DTT, 5DVA


• PubMed Abstract: 
  

  The spread of antibiotic resistant bacteria is a global threat that shakes the foundations of modern healthcare. β-Lactamases are enzymes that confer resistance to β-lactam antibiotics in bacteria, and there is a critical need for new inhibitors of these enzymes for combination therapy together with an antibiotic. With this in mind, we have screened a library of 490 fragments to identify starting points for the development of new inhibitors of the class D β-lactamase oxacillinase-48 (OXA-48) through surface plasmon resonance (SPR), dose-rate inhibition assays, and X-ray crystallography. Furthermore, we have uncovered structure-activity relationships and used alternate conformations from a crystallographic structure to grow a fragment into a more potent compound with a KD of 50 μM and an IC50 of 18 μM.

---

Organizational Affiliation: 
• The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway , 9037 Tromsø, Norway.
Department of Chemistry, UiT The Arctic University of Norway , 9037 Tromsø, Norway.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 123.74 kDa 
• Atom Count: 9,524 
• Modeled Residue Count: 972 
• Deposited Residue Count: 1,060 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	265	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: bla OXA-48, blaOXA-48, KPE71T_00045 EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae) Explore Q6XEC0  Go to UniProtKB:  Q6XEC0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5F3	J [auth A], K [auth B], U [auth C], V [auth D]	3,5-di(pyridin-4-yl)benzoic acid C17 H12 N2 O2 NNTKTJCJOPINGZ-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], W [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A], O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.172 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.523	α = 90
b = 124.31	β = 98.263
c = 108.742	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Lund, B.A., Christopeit, T., Leiros, H.-K.S.

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2016-06-22
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description