7UOX

NDM1-inhibitor co-structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.137 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Rapid Evolution of a Fragment-like Molecule to Pan-Metallo-Beta-Lactamase Inhibitors: Initial Leads toward Clinical Candidates.

Mandal, M.Xiao, L.Pan, W.Scapin, G.Li, G.Tang, H.Yang, S.W.Pan, J.Root, Y.de Jesus, R.K.Yang, C.Prosise, W.Dayananth, P.Mirza, A.Therien, A.G.Young, K.Flattery, A.Garlisi, C.Zhang, R.Chu, D.Sheth, P.Chu, I.Wu, J.Markgraf, C.Kim, H.Y.Painter, R.Mayhood, T.W.DiNunzio, E.Wyss, D.F.Buevich, A.V.Fischmann, T.Pasternak, A.Dong, S.Hicks, J.D.Villafania, A.Liang, L.Murgolo, N.Black, T.Hagmann, W.K.Tata, J.Parmee, E.R.Weber, A.E.Su, J.Tang, H.

(2022) J Med Chem 65: 16234-16251

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00766
  • Primary Citation of Related Structures:  
    7UOX, 7UOY, 7UP1, 7UP2, 7UP3

  • PubMed Abstract: 

    With the emergence and rapid spreading of NDM-1 and existence of clinically relevant VIM-1 and IMP-1, discovery of pan inhibitors targeting metallo-beta-lactamases (MBLs) became critical in our battle against bacterial infection. Concurrent with our fragment and high-throughput screenings, we performed a knowledge-based search of known metallo-beta-lactamase inhibitors (MBLIs) to identify starting points for early engagement of medicinal chemistry. A class of compounds exemplified by 11 , discovered earlier as B. fragilis metallo-beta-lactamase inhibitors, was selected for in silico virtual screening. From these efforts, compound 12 was identified with activity against NDM-1 only. Initial exploration on metal binding design followed by structure-guided optimization led to the discovery of a series of compounds represented by 23 with a pan MBL inhibition profile. In in vivo studies, compound 23 in combination with imipenem (IPM) robustly lowered the bacterial burden in a murine infection model and became the lead for the invention of MBLI clinical candidates.


  • Organizational Affiliation

    Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey07033, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metallo beta-lactamase
A, B
248Klebsiella pneumoniaeMutation(s): 0 
Gene Names: 
EC: 3.5.2.6
UniProt
Find proteins for E9NWK5 (Klebsiella pneumoniae)
Explore E9NWK5 
Go to UniProtKB:  E9NWK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9NWK5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O0L (Subject of Investigation/LOI)
Query on O0L

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
(2M)-4'-(hydroxymethyl)-2-(1H-tetrazol-5-yl)[1,1'-biphenyl]-3-ol
C14 H12 N4 O2
MHFBCDLPGNNTMV-UHFFFAOYSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
M [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.03α = 90
b = 78.81β = 90
c = 134.81γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
BUSTERphasing

Structure Validation

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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: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description