9C5P | pdb_00009c5p

Inhibitor bound VIM1

• PDB DOI: https://doi.org/10.2210/pdb9C5P/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-06 Released: 2024-10-16 
• Deposition Author(s): Fischmann, T.O., Scapin, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.175 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Discovery of sulfone containing metallo-beta-lactamase inhibitors with reduced bacterial cell efflux and histamine release issues.

Bennett, F., Huang, Y., Dong, S., Jiang, J., Hunter, D., Zhao, Z., Gu, X., Scott, J.D., Tang, H., Yang, D., Xiao, L., Scapin, G., Fischmann, T., Mirza, A., Dayananth, P., Painter, R.E., Villafania, A., Garlisi, C.G., Zhang, R., Mayhood, T.W., Si, Q., Li, N., Amin, R.P., Chen, F., Bhatt, B., Regan, C.P., Regan, H., Lin, X., Wu, J., Leithead, A., Young, K., Pasternak, A.

(2024) Bioorg Med Chem Lett 114: 129989-129989

• PubMed: 39396683 
• DOI: https://doi.org/10.1016/j.bmcl.2024.129989
• Primary Citation of Related Structures:  
  9C5P


• PubMed Abstract: 
  

  The design, syntheses and antibacterial evaluation of sulfone analogues of previously disclosed metallo-β-lactamase inhibitors (MBLis) are described. The novel derivatives were overall more effective in gram-negative bacterial cell-based assays when combined with imipenem and relebactam. The major contributors to the improved anti-bacterial activity are enhanced enzyme-inhibitor interactions and reduced bacterial cell efflux monitored via an efflux assay involving isogenic Pseudomonas aeruginosa efflux + and efflux - tool strains.

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Organizational Affiliation: 
• Merck & Co., Inc., Department of Medicinal Chemistry, 126 E. Lincoln Avenue, Rahway, NJ 07065, USA. Electronic address: [e-mail].
Merck & Co., Inc., Department of Medicinal Chemistry, 126 E. Lincoln Avenue, Rahway, NJ 07065, USA.
Merck & Co., Inc., Department of Computational and Structural Chemistry, 126 E. Lincoln Avenue., Rahway, NJ 07065, USA.
Merck & Co., Inc., Department of Infectious Diseases, 770 Sumneytown Pike., West Point, PA 19486, USA.
Merck & Co., Inc., Department of Pharmacology, 770 Sumneytown Pike, West Point, PA 19486, USA.
Merck & Co., Inc., Department of Nonclinical Drug Safety, 770 Sumneytown Pike, West Point, PA 19486, USA.
Merck & Co., Inc., Department of Pharmacokinetics and Pharmacodynamics, 770 Sumneytown Pike, West Point, PA 19486, USA.
Merck & Co., Inc., Department of Pharmaceutical Sciences, 770 Sumneytown Pike, West Point, PA 19486, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.75 kDa 
• Atom Count: 2,108 
• Modeled Residue Count: 231 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase type 2	A	246	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: vim5 EC: 3.5.2.6
UniProt
Find proteins for A0A0F7KYQ8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore A0A0F7KYQ8  Go to UniProtKB:  A0A0F7KYQ8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AUQ (Subject of Investigation/LOI)	E [auth A]	(2M)-4-(piperidine-4-sulfonyl)-4'-(piperidin-4-yl)-2-(1H-tetrazol-5-yl)[1,1'-biphenyl]-3-sulfonamide C23 H29 N7 O4 S2 MMQDOCFJJIBSMW-UHFFFAOYSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.175 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.61	α = 90
b = 67.88	β = 91.44
c = 40.17	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
BUSTER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Fischmann, T.O., Scapin, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Database references