9DAG | pdb_00009dag

Crystal structure of NDM-1 complexed with compound 13

PDB DOI: https://doi.org/10.2210/pdb9DAG/pdb

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

Deposited: 2024-08-22 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.222 (Depositor), 0.226 (DCC)
R-Value Work:
0.163 (Depositor), 0.170 (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: 25.6 kDa
Atom Count: 1,889
Modeled Residue Count: 229
Deposited Residue Count: 233
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7C422
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A3B (Subject of Investigation/LOI) Query on A1A3B Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain B [auth A]	B [auth A], E [auth A]	{[6-fluoro-1-methyl-2-oxo-7-(pyrrolidin-1-yl)-1,2-dihydroquinolin-4-yl]methyl}phosphonic acid C₁₅ H₁₈ F N₂ O₄ P MLFCPSYHIKBWQX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]