7UYD | pdb_00007uyd

Inhibitor bound VIM1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 
    0.161 (Depositor), 0.151 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7UYD

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: 52.18 kDa 
  • Atom Count: 4,264 
  • Modeled Residue Count: 464 
  • Deposited Residue Count: 480 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase VIM-2-like protein
A, B
240Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIM
EC: 3.5.2.6
UniProt
Find proteins for B8QIQ9 (Pseudomonas aeruginosa)
Explore B8QIQ9 
Go to UniProtKB:  B8QIQ9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8QIQ9
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
J [auth A]
K [auth A]
L [auth A]
T [auth B]
U [auth B]
J [auth A],
K [auth A],
L [auth A],
T [auth B],
U [auth B],
V [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
M [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
Q [auth B]
R [auth B]
G [auth A],
H [auth A],
I [auth A],
Q [auth B],
R [auth B],
S [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free:  0.161 (Depositor), 0.151 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.652α = 90
b = 78.957β = 130.52
c = 67.764γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
BUSTERphasing

Structure Validation

View Full Validation Report



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