7UYA | pdb_00007uya

Inhibitor bound VIM1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 
    0.179 (Depositor), 0.174 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7UYA

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure Guided Discovery of Novel Pan Metallo-beta-Lactamase Inhibitors with Improved Gram-Negative Bacterial Cell Penetration.

Dong, S.Zhao, Z.Tang, H.Li, G.Pan, J.Gu, X.Jiang, J.Xiao, L.Scapin, G.Hunter, D.N.Yang, D.Huang, Y.Bennett, F.Yang, S.W.Mandal, M.Tang, H.Su, J.Tudge, C.deJesus, R.K.Ding, F.X.Lombardo, M.Hicks, J.D.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.Bhatt, B.Chen, F.Regan, C.P.Regan, H.Lin, X.Wu, J.Leithead, A.Pollack, S.R.Scott, J.D.Nargund, R.P.Therien, A.G.Black, T.Young, K.Pasternak, A.

(2024) J Med Chem 67: 3400-3418

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01614
  • Primary Citation Related Structures: 
    7UYA, 7UYB, 7UYC, 7UYD

  • PubMed Abstract: 

    The use of β-lactam (BL) and β-lactamase inhibitor combination to overcome BL antibiotic resistance has been validated through clinically approved drug products. However, unmet medical needs still exist for the treatment of infections caused by Gram-negative (GN) bacteria expressing metallo-β-lactamases. Previously, we reported our effort to discover pan inhibitors of three main families in this class: IMP, VIM, and NDM. Herein, we describe our work to improve the GN coverage spectrum in combination with imipenem and relebactam. This was achieved through structure- and property-based optimization to tackle the GN cell penetration and efflux challenges. A significant discovery was made that inhibition of both VIM alleles, VIM-1 and VIM-2, is essential for broad GN coverage, especially against VIM-producing P. aeruginosa . In addition, pharmacokinetics and nonclinical safety profiles were investigated for select compounds. Key findings from this drug discovery campaign laid the foundation for further lead optimization toward identification of preclinical candidates.


  • Organizational Affiliation
    • Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States.

Macromolecule Content 

  • Total Structure Weight: 26.53 kDa 
  • Atom Count: 2,067 
  • Modeled Residue Count: 230 
  • Deposited Residue Count: 246 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase VIM-1246Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIMblaVIM-1CAZ10_38240CAZ10_38245
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F7KYQ8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free:  0.179 (Depositor), 0.174 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.53α = 90
b = 67.565β = 91.66
c = 40.102γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Database references