Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 83.34 kDa 
• Atom Count: 5984 
• Modelled Residue Count: 704 
• Deposited Residue Count: 732 
• Unique protein chains: 1

4R3N

Crystal structure of the ternary complex of sp-ASADH with NADP and 1,2,3-Benzenetricarboxylic acid

• PDB DOI: 10.2210/pdb4R3N/pdb

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


• Deposited: 2014-08-16 Released: 2014-12-10 
• Deposition Author(s): Pavlovsky, A.G., Viola, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.161 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 

Literature

A cautionary tale of structure-guided inhibitor development against an essential enzyme in the aspartate-biosynthetic pathway.

Pavlovsky, A.G., Thangavelu, B., Bhansali, P., Viola, R.E.

(2014) Acta Crystallogr D Biol Crystallogr 70: 3244-3252

• PubMed: 25478842 
• DOI: 10.1107/S1399004714023979
• Primary Citation of Related Structures:  
  4R3N, 4R3W, 4R41, 4R4J, 4R51, 4R54, 4R5H, 4R5M


• PubMed Abstract: 
  

The aspartate pathway is essential for the production of the amino acids required for protein synthesis and of the metabolites needed in bacterial development. This pathway also leads to the production of several classes of quorum-sensing molecules that can trigger virulence in certain microorganisms. The second enzyme in this pathway, aspartate β-semialdehyde dehydrogenase (ASADH), is absolutely required for bacterial survival and has been targeted for the design of selective inhibitors. Fragment-library screening has identified a new set of inhibitors that, while they do not resemble the substrates for this reaction, have been shown to bind at the active site of ASADH. Structure-guided development of these lead compounds has produced moderate inhibitors of the target enzyme, with some selectivity observed between the Gram-negative and Gram-positive orthologs of ASADH. However, many of these inhibitor analogs and derivatives have not yet achieved the expected enhanced affinity. Structural characterization of these enzyme-inhibitor complexes has provided detailed explanations for the barriers that interfere with optimal binding. Despite binding in the same active-site region, significant changes are observed in the orientation of these bound inhibitors that are caused by relatively modest structural alterations. Taken together, these studies present a cautionary tale for issues that can arise in the systematic approach to the modification of lead compounds that are being used to develop potent inhibitors.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate-semialdehyde dehydrogenase	A, B	366	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: asd EC: 1.2.1.11
UniProt
Find proteins for Q8DQ00 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DQ00  Go to UniProtKB:  Q8DQ00

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], K [auth B], L [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
3GQ	F [auth A], M [auth B]	benzene-1,2,3-tricarboxylic acid C9 H6 O6 UJMDYLWCYJJYMO-UHFFFAOYSA-N
EDO	G [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	H [auth A], I [auth A], R [auth B], S [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	C [auth A], D [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3GQ	Binding MOAD:  4R3N	Ki: 1.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.161 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.536	α = 90
b = 97.658	β = 102.55
c = 63.978	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-08-16 
• Released Date: 2014-12-10 
Deposition Author(s): Pavlovsky, A.G., Viola, R.E.

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description