6AHE

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

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Literature

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: 10.1111/cbdd.13686
  • Primary Citation of Related Structures:  
    6AHE

  • 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 ...

    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: 

    Aurigene Discovery Technologies Ltd, Bangalore, India.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]A,
D [auth B],
C,
B [auth D]		267Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: NC_009085.1, fabI, HMPREF0010_01715
EC: 1.3.1.9
UniProt
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
E [auth A],
G [auth D],
I [auth C],
K [auth B]		NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N		 Ligand Interaction
0WE
Query on 0WE
Download Ideal Coordinates CCD File 
F [auth A],
H [auth D],
J [auth C],
L [auth B]		N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)propanamide
C22 H23 N3 O3
WDNCPCMRTFYNIQ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing

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