5DRO | pdb_00005dro

Structure of the Aquifex aeolicus LpxC/LPC-011 Complex

• PDB DOI: https://doi.org/10.2210/pdb5DRO/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-09-16 Released: 2016-03-09 
• Deposition Author(s): Lee, C.-J., Najeeb, J., Zhou, P.
• 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: 2.01 Å
• R-Value Free: 
  0.186 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Drug design from the cryptic inhibitor envelope.

Lee, C.J., Liang, X., Wu, Q., Najeeb, J., Zhao, J., Gopalaswamy, R., Titecat, M., Sebbane, F., Lemaitre, N., Toone, E.J., Zhou, P.

(2016) Nat Commun 7: 10638-10638

• PubMed: 26912110 
• DOI: https://doi.org/10.1038/ncomms10638
• Primary Citation Related Structures: 
  5DRO, 5DRP, 5DRQ, 5DRR


• PubMed Abstract: 
  

  Conformational dynamics plays an important role in enzyme catalysis, allosteric regulation of protein functions and assembly of macromolecular complexes. Despite these well-established roles, such information has yet to be exploited for drug design. Here we show by nuclear magnetic resonance spectroscopy that inhibitors of LpxC--an essential enzyme of the lipid A biosynthetic pathway in Gram-negative bacteria and a validated novel antibiotic target--access alternative, minor population states in solution in addition to the ligand conformation observed in crystal structures. These conformations collectively delineate an inhibitor envelope that is invisible to crystallography, but is dynamically accessible by small molecules in solution. Drug design exploiting such a hidden inhibitor envelope has led to the development of potent antibiotics with inhibition constants in the single-digit picomolar range. The principle of the cryptic inhibitor envelope approach may be broadly applicable to other lead optimization campaigns to yield improved therapeutics.

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Organizational Affiliation: 
• Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.
Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
Inserm, Univ. Lille, CHU Lille, Institut Pasteur de Lille, CNRS, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.73 kDa 
• Atom Count: 4,840 
• Modeled Residue Count: 534 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase	A, B	274	Aquifex aeolicus VF5	Mutation(s): 1  Gene Names: lpxC, envA, aq_1772 EC: 3.5.1 (PDB Primary Data), 3.5.1.108 (UniProt)
UniProt
Find proteins for O67648 (Aquifex aeolicus (strain VF5)) Explore O67648  Go to UniProtKB:  O67648

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZH2	D [auth A], G [auth B]	4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]benzamide C21 H19 N3 O4 SNVYDNOGPYZQEV-KUHUBIRLSA-N
DMS	E [auth A], I [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.186 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.82	α = 90
b = 74.68	β = 90
c = 135.87	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Lee, C.-J., Najeeb, J., Zhou, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI055588
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI094475

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description