5I9M

Crystal structure of B. pseudomallei FabI in complex with NAD and PT408


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase.

Eltschkner, S.Cummings, J.E.Hirschbeck, M.Daryaee, F.Bommineni, G.R.Zhang, Z.Spagnuolo, L.Yu, W.Davoodi, S.Slayden, R.A.Kisker, C.Tonge, P.J.Neckles, C.

(2017) Biochemistry 56: 1865-1878

  • DOI: 10.1021/acs.biochem.6b01048
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • There is growing awareness of the link between drug-target residence time and in vivo drug activity, and there are increasing efforts to determine the molecular factors that control the lifetime of a drug-target complex. Rational alterations in the d ...

    There is growing awareness of the link between drug-target residence time and in vivo drug activity, and there are increasing efforts to determine the molecular factors that control the lifetime of a drug-target complex. Rational alterations in the drug-target residence time require knowledge of both the ground and transition states on the inhibition reaction coordinate, and we have determined the structure-kinetic relationship for 22 ethyl- or hexyl-substituted diphenyl ethers that are slow-binding inhibitors of bpFabI1, the enoyl-ACP reductase FabI1 from Burkholderia pseudomallei. Analysis of enzyme inhibition using a two-dimensional kinetic map demonstrates that the ethyl and hexyl diphenyl ethers fall into two distinct clusters. Modifications to the ethyl diphenyl ether B ring result in changes to both on and off rates, where residence times of up to ∼700 min (∼11 h) are achieved by either ground state stabilization (PT444) or transition state destabilization (slower on rate) (PT404). By contrast, modifications to the hexyl diphenyl ether B ring result in residence times of 300 min (∼5 h) through changes in only ground state stabilization (PT119). Structural analysis of nine enzyme:inhibitor complexes reveals that the variation in structure-kinetic relationships can be rationalized by structural rearrangements of bpFabI1 and subtle changes to the orientation of the inhibitor in the binding pocket. Finally, we demonstrate that three compounds with residence times on bpFabI1 from 118 min (∼2 h) to 670 min (∼11 h) have in vivo efficacy in an acute B. pseudomallei murine infection model using the virulent B. pseudomallei strain Bp400.


    Organizational Affiliation

    Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enoyl-[acyl-carrier-protein] reductase [NADH]
A, B, C
276Burkholderia pseudomallei (strain 1026b)Mutation(s): 0 
Gene Names: fabI
EC: 1.3.1.9
Find proteins for A0A0H3HP34 (Burkholderia pseudomallei (strain 1026b))
Go to UniProtKB:  A0A0H3HP34
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
69K
Query on 69K

Download SDF File 
Download CCD File 
A, B, C
5-ethyl-4-fluoro-2-[(2-methylpyridin-3-yl)oxy]phenol
C14 H14 F N O2
VHXDJFGLVVJBNS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
69KKi: 55 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.251 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 69.029α = 90.00
b = 111.217β = 90.00
c = 260.695γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Germany--

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-08
    Type: Database references
  • Version 1.2: 2017-04-19
    Type: Database references