Crystal structure of enoyl-ACP reductase from Acinetobacter baumannii in complex with NAD and AFN-1252

Experimental Data Snapshot

  • Resolution: 2.29 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

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Ternary complex formation of AFN-1252 with Acinetobacter baumannii FabI and NADH: Crystallographic and biochemical studies.

Rao, N.K.Nataraj, V.Ravi, M.Panchariya, L.Palai, K.Talapati, S.R.Lakshminarasimhan, A.Ramachandra, M.Antony, T.

(2020) Chem Biol Drug Des 96: 704-713

  • DOI: https://doi.org/10.1111/cbdd.13686
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Acinetobacter baumannii is an opportunistic Gram-negative bacterial pathogen, associated mostly with hospital-acquired infections. The emergence of drug resistance strains made it necessary to explore new pathways for the development of more effective antibiotics. Enoyl CoA reductase (FabI), a key enzyme in the fatty acid biosynthesis (FAS) pathway, has emerged as a potential target for antibacterial drug development. Earlier reports show that the lead SaFabI inhibitor AFN-1252 can inhibit FabI from other organisms including Escherichia coli and Burkholderia pseudomallei, but with differential potency. In the present work, we show that AFN-1252 is a moderate inhibitor of AbFabI with an IC 50 of 216 nM. AFN-1252 stabilized AbFabI with a 4.2°C increase in the melting temperature (T m ) and, interestingly, the stabilization effect was significantly increased in presence of the cofactor NADH (∆T m  = 17°C), suggesting the formation of a ternary complex AbFabI: AFN-1252: NADH. X-ray crystallography studies of AbFabI co-crystalized with AFN-1252 and NADH confirmed the ternary complex formation. The critical interactions of AFN-1252 with AbFabI and NADH identified from the co-crystal structure may facilitate the design and development of new drugs against A. baumannii infections by targeting the FAS pathway.

  • Organizational Affiliation

    International Center for Genetic Engineering and Biotechnology, New Delhi, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]A,
B [auth D],
D [auth B]
267Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: NC_009085.1fabIHMPREF0010_01715
Find proteins for D0CAD5 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
Explore D0CAD5 
Go to UniProtKB:  D0CAD5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0CAD5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.29 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.529α = 90
b = 89.573β = 90
c = 159.473γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description