9D5R | pdb_00009d5r

Crystal structure of KPC-2 complexed with compound 22

PDB DOI: https://doi.org/10.2210/pdb9D5R/pdb

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

Deposited: 2024-08-14 Released: 2025-08-20
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.191 (Depositor), 0.200 (DCC)
R-Value Work:
0.154 (Depositor), 0.165 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure-Based Design of Reversible, Quinoline-2(1H)-one Inhibitors of Serine- and Metallo-Carbapenemases

Jacobs, L.M.C., Jaishankar, P., Zheng, J., Hantz, E.R., Lee, I., Narramneni, K., Poore, N., Torres, N., Jackson, J.K., Williams, O., Darch, S.E., Shaw, L.N., Chen, Y., Renslo, A.R.

(2026) ACS Omega 11: 15316-15327

DOI: https://doi.org/10.1021/acsomega.5c12676

Macromolecule Content

Total Structure Weight: 31.69 kDa
Atom Count: 2,280
Modeled Residue Count: 269
Deposited Residue Count: 290
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9F663
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A14 (Subject of Investigation/LOI) Query on A1A14 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	{[7-bromo-1-(cyclopentylmethyl)-3-methyl-2-oxo-1,2-dihydroquinolin-4-yl]methyl}phosphonic acid C₁₇ H₂₁ Br N O₄ P NQLOLOZBNRHGEE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	C [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]