6LJ5 | pdb_00006lj5

Crystal structure of NDM-1 in complex with D-captopril derivative wss04145

• PDB DOI: https://doi.org/10.2210/pdb6LJ5/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-12-13 Released: 2020-12-16 
• Deposition Author(s): Zhang, H., Ma, G.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Structure-guided optimization of D-captopril for discovery of potent NDM-1 inhibitors.

Ma, G., Wang, S., Wu, K., Zhang, W., Ahmad, A., Hao, Q., Lei, X., Zhang, H.

(2020) Bioorg Med Chem 29: 115902-115902

• PubMed: 33302045 
• DOI: https://doi.org/10.1016/j.bmc.2020.115902
• Primary Citation of Related Structures:  
  6LIP, 6LIZ, 6LJ0, 6LJ1, 6LJ2, 6LJ4, 6LJ5, 6LJ6, 6LJ7, 6LJ8


• PubMed Abstract: 
  

  β-lactam antibiotics have long been the mainstay for the treatment of bacterial infections. New Delhi metallo-β-lactamase 1 (NDM-1) is able to hydrolyze nearly all β-lactam antibiotics and even clinically used serine-β-lactamase inhibitors. The wide and rapid spreading of NDM-1 gene among pathogenic bacteria has attracted extensive attention, therefore high potency NDM-1 inhibitors are urgently needed. Here we report a series of structure-guided design of D-captopril derivatives that can inhibit the activity of NDM-1 in vitro and at cellular levels. Structural comparison indicates the mechanisms of inhibition enhancement and provides insights for further inhibitor optimization.

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Organizational Affiliation: 
• Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research and Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
School of Biomedical Sciences, The University of Hong Kong, Hong Kong Special Administrative Region.
School of Biomedical Sciences, The University of Hong Kong, Hong Kong Special Administrative Region. Electronic address: [e-mail].
Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address: [e-mail].
Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research and Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.06 kDa 
• Atom Count: 2,054 
• Modeled Residue Count: 229 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase type 2	A	242	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EF0 (Subject of Investigation/LOI)	C [auth A]	1-[(2S)-2-methyl-3-sulfanyl-propanoyl]piperidine-4-carboxylic acid C10 H17 N O3 S VYYKYNRWNVSARB-SSDOTTSWSA-N
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.785	α = 90
b = 60.015	β = 98.48
c = 42.321	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Zhang, H., Ma, G.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31670753

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2020-12-23
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description