9D54 | pdb_00009d54

Crystal structure of KPC-2 complexed with compound 12

• PDB DOI: https://doi.org/10.2210/pdb9D54/pdb

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


• Deposited: 2024-08-13 Released: 2025-10-29 
• 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: 1.60 Å
• R-Value Free: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.154 (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: 31.5 kDa 
• Atom Count: 2,308 
• Modeled Residue Count: 269 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbapenem-hydrolyzing beta-lactamase KPC	A	290	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: bla, kpc, kpc1 EC: 3.5.2.6
UniProt
Find proteins for Q9F663 (Klebsiella pneumoniae) Explore Q9F663  Go to UniProtKB:  Q9F663

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1A22 (Subject of Investigation/LOI)	B [auth A]	[(7-cyclopropyl-6-fluoro-1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)methyl]phosphonic acid C14 H15 F N O4 P LWVVYRFECQFPGI-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.446	α = 90
b = 59.734	β = 90
c = 78.763	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
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: 2025-10-29
  Type: Initial release