Salicylate Adenylate PchD from Pseudomonas aeruginosa containing 4-cyanosalicyl-AMS

Experimental Data Snapshot

  • Resolution: 1.69 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Rational inhibitor design for Pseudomonas aeruginosa salicylate adenylation enzyme PchD.

Shelton, C.L.Meneely, K.M.Ronnebaum, T.A.Chilton, A.S.Riley, A.P.Prisinzano, T.E.Lamb, A.L.

(2022) J Biol Inorg Chem 27: 541-551

  • DOI: https://doi.org/10.1007/s00775-022-01941-8
  • Primary Citation of Related Structures:  
    7TYB, 7TZ4

  • PubMed Abstract: 

    Pseudomonas aeruginosa is an increasingly antibiotic-resistant pathogen that causes severe lung infections, burn wound infections, and diabetic foot infections. P. aeruginosa produces the siderophore pyochelin through the use of a non-ribosomal peptide synthetase (NRPS) biosynthetic pathway. Targeting members of siderophore NRPS proteins is one avenue currently under investigation for the development of new antibiotics against antibiotic-resistant organisms. Here, the crystal structure of the pyochelin adenylation domain PchD is reported. The structure was solved to 2.11 Å when co-crystallized with the adenylation inhibitor 5'-O-(N-salicylsulfamoyl)adenosine (salicyl-AMS) and to 1.69 Å with a modified version of salicyl-AMS designed to target an active site cysteine (4-cyano-salicyl-AMS). In the structures, PchD adopts the adenylation conformation, similar to that reported for AB3403 from Acinetobacter baumannii.

  • Organizational Affiliation

    Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyochelin biosynthesis salicyl-AMP ligase PchD547Pseudomonas aeruginosaMutation(s): 0 
Gene Names: pchDLYSZa2_15910LYSZa5_15910
EC: 2.7.7
Find proteins for Q9HWG3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HWG3 
Go to UniProtKB:  Q9HWG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HWG3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KUX (Subject of Investigation/LOI)
Query on KUX

Download Ideal Coordinates CCD File 
B [auth A]5'-O-[(4-cyano-2-hydroxybenzoyl)sulfamoyl]adenosine
C18 H17 N7 O8 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.69 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.06α = 90
b = 44.854β = 99.18
c = 66.615γ = 90
Software Package:
Software NamePurpose
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM127655
National Science Foundation (NSF, United States)United States1904494
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK12GM063651

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description