9D5Q | pdb_00009d5q

Crystal structure of KPC-2 complexed with compound 21

PDB DOI: https://doi.org/10.2210/pdb9D5Q/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: 1.99 Å
R-Value Free:
0.205 (Depositor), 0.215 (DCC)
R-Value Work:
0.163 (Depositor), 0.172 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 32.01 kDa
Atom Count: 2,268
Modeled Residue Count: 269
Deposited Residue Count: 290
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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
A1A13 (Subject of Investigation/LOI) Query on A1A13 Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	({7-bromo-2-oxo-1-[(1Z)-3-phenylprop-1-en-1-yl]-1,2-dihydroquinolin-4-yl}methyl)phosphonic acid C₁₉ H₁₇ Br N O₄ P DMPGYOUGLIOHKL-WMZJFQQLSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] F [auth A] G [auth A] B [auth A], C [auth A], D [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]