7UT5

Acinetobacter baumannii dihydroorotate dehydrogenase bound with inhibitor DSM186


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Repurposed dihydroorotate dehydrogenase inhibitors with efficacy against drug-resistant Acinetobacter baumannii.

Russo, T.A.Umland, T.C.Deng, X.El Mazouni, F.Kokkonda, S.Olson, R.Carlino-MacDonald, U.Beanan, J.Alvarado, C.L.Tomchick, D.R.Hutson, A.Chen, H.Posner, B.Rathod, P.K.Charman, S.A.Phillips, M.A.

(2022) Proc Natl Acad Sci U S A 119: e2213116119-e2213116119

  • DOI: https://doi.org/10.1073/pnas.2213116119
  • Primary Citation of Related Structures:  
    7UT5

  • PubMed Abstract: 

    New antimicrobials are needed for the treatment of extensively drug-resistant Acinetobacter baumannii . The de novo pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) is a validated drug target for malaria and human autoimmune diseases. We provide genetic evidence that A. baumannii DHODH ( Ab DHODH) is essential for bacterial survival in rodent infection models. We chemically validate the target by repurposing a unique library of ~450 triazolopyrimidine/imidazopyrimidine analogs developed for our malaria DHODH program to identify 21 compounds with submicromolar activity on Ab DHODH. The most potent (DSM186, DHODH IC 50 28 nM) had a minimal inhibitory concentration of ≤1 µg/ml against geographically diverse A. baumannii strains, including meropenem-resistant isolates. A structurally related analog (DSM161) with a long in vivo half-life conferred significant protection in the neutropenic mouse thigh infection model. Encouragingly, the development of resistance to these compounds was not identified in vitro or in vivo. Lastly, the X-ray structure of Ab DHODH bound to DSM186 was solved to 1.4 Å resolution. These data support the potential of Ab DHODH as a drug target for the development of antimicrobials for the treatment of A. baumannii and potentially other high-risk bacterial infections.


  • Organizational Affiliation

    Department of Medicine, Veterans Administration Western New York Healthcare System, Buffalo, NY 14215.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone)
A, B
354Acinetobacter baumanniiMutation(s): 0 
Gene Names: pyrDABBFA_001187
EC: 1.3.5.2
UniProt
Find proteins for B7GZW7 (Acinetobacter baumannii (strain AB307-0294))
Explore B7GZW7 
Go to UniProtKB:  B7GZW7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7GZW7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
OBR (Subject of Investigation/LOI)
Query on OBR

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
(4R)-7-methyl-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl]imidazo[1,2-a]pyrimidin-5-amine
C13 H11 F5 N4 S
WQQKDMYAYLYJLV-UHFFFAOYSA-N
ORO
Query on ORO

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.53α = 90
b = 89.77β = 90.036
c = 84.417γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

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 Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI103947
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56AI129986

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description