9DE3 | pdb_00009de3

Crystal structure of NDM-1 complexed with compound 28

• PDB DOI: https://doi.org/10.2210/pdb9DE3/pdb

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


• Deposited: 2024-08-28 Released: 2025-09-03 
• Deposition Author(s): Jacobs, L.M.C., Chen, Y.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.256 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Hit to Lead Optimization of Heteroaryl Phosphonates Reversible, Broad-Spectrum Inhibitors of Serine and Metallo Carbapenemases.

Jacobs, L.M.C., Chen, Y., Renslo, A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.14 kDa 
• Atom Count: 1,791 
• Modeled Residue Count: 229 
• Deposited Residue Count: 233 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase type 2	A	233	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaNDM-1 EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae) Explore C7C422  Go to UniProtKB:  C7C422

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1A4C (Subject of Investigation/LOI)	B [auth A]	{[1-(cyclopentylmethyl)-3-methyl-2-oxo-7-(pyrrolidin-1-yl)-1,2-dihydroquinolin-4-yl]methyl}phosphonic acid C21 H29 N2 O4 P BDTXVWMOHGBEPP-UHFFFAOYSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.256 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.39	α = 90
b = 59.702	β = 97.85
c = 41.643	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Jacobs, L.M.C., Chen, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R01AI103158-01A1

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release