Crystal Structure of Aspartate beta-Semialdehide Dehydrogenase from Streptococcus pneumoniae with 2',5'-Adenosine diphosphate and D-2-aminoadipate

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structural Characterization of Inhibitors with Selectivity against Members of a Homologous Enzyme Family.

Pavlovsky, A.G.Liu, X.Faehnle, C.R.Potente, N.Viola, R.E.

(2012) Chem Biol Drug Des 79: 128-136

  • DOI: https://doi.org/10.1111/j.1747-0285.2011.01267.x
  • Primary Citation of Related Structures:  
    3PWK, 3PWS, 3PYL, 3PYX, 3PZB, 3PZR, 3Q0E, 3Q11, 3Q1L

  • PubMed Abstract: 

    The aspartate biosynthetic pathway provides essential metabolites for many important biological functions, including the production of four essential amino acids. As this critical pathway is only present in plants and microbes, any disruptions will be fatal to these organisms. An early pathway enzyme, l-aspartate-β-semialdehyde dehydrogenase, produces a key intermediate at the first branch point of this pathway. Developing potent and selective inhibitors against several orthologs in the l-aspartate-β-semialdehyde dehydrogenase family can serve as lead compounds for antibiotic development. Kinetic studies of two small molecule fragment libraries have identified inhibitors that show good selectivity against l-aspartate-β-semialdehyde dehydrogenases from two different bacterial species, Streptococcus pneumoniae and Vibrio cholerae, despite the presence of an identical constellation of active site amino acids in this homologous enzyme family. Structural characterization of enzyme-inhibitor complexes have elucidated different modes of binding between these structurally related enzymes. This information provides the basis for a structure-guided approach to the development of more potent and more selective inhibitors.

  • Organizational Affiliation

    Department of Chemistry, University of Toledo, Toledo, OH 43606, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate-semialdehyde dehydrogenase
A, B
366Streptococcus pneumoniae SP23-BS72Mutation(s): 0 
Gene Names: CGSSp23BS72_03388
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 25A

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
C30 H38 N15 O19 P3
Query on L14

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
trans-cyclohexane-1,4-dicarboxylic acid
C8 H12 O4
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
C2 H6 O2
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
P [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
L14 Binding MOAD:  3PWK Ki: 4.50e+5 (nM) from 1 assay(s)
PDBBind:  3PWK Ki: 4.50e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.872α = 90
b = 99.66β = 100.91
c = 64.436γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-04
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description