4BNJ

Crystal structure of S. aureus FabI in complex with NADP and 5-methyl- 2-phenoxyphenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rational Optimization of Drug-Target Residence Time: Insights from Inhibitor Binding to the S. Aureus Fabi Enzyme-Product Complex.

Chang, A.Schiebel, J.Yu, W.Bommineni, G.R.Pan, P.Baxter, M.V.Khanna, A.Sotriffer, C.A.Kisker, C.F.Tonge, P.J.

(2013) Biochemistry 52: 4217

  • DOI: 10.1021/bi400413c
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Drug-target kinetics has recently emerged as an especially important facet of the drug discovery process. In particular, prolonged drug-target residence times may confer enhanced efficacy and selectivity in the open in vivo system. However, the lack ...

    Drug-target kinetics has recently emerged as an especially important facet of the drug discovery process. In particular, prolonged drug-target residence times may confer enhanced efficacy and selectivity in the open in vivo system. However, the lack of accurate kinetic and structural data for a series of congeneric compounds hinders the rational design of inhibitors with decreased off-rates. Therefore, we chose the Staphylococcus aureus enoyl-ACP reductase (saFabI)--an important target for the development of new anti-staphylococcal drugs--as a model system to rationalize and optimize the drug-target residence time on a structural basis. Using our new, efficient, and widely applicable mechanistically informed kinetic approach, we obtained a full characterization of saFabI inhibition by a series of 20 diphenyl ethers complemented by a collection of 9 saFabI-inhibitor crystal structures. We identified a strong correlation between the affinities of the investigated saFabI diphenyl ether inhibitors and their corresponding residence times, which can be rationalized on a structural basis. Because of its favorable interactions with the enzyme, the residence time of our most potent compound exceeds 10 h. In addition, we found that affinity and residence time in this system can be significantly enhanced by modifications predictable by a careful consideration of catalysis. Our study provides a blueprint for investigating and prolonging drug-target kinetics and may aid in the rational design of long-residence-time inhibitors targeting the essential saFabI enzyme.


    Organizational Affiliation

    Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
A, B, C, D, E, F, G, H
282Staphylococcus aureus (strain N315)Mutation(s): 1 
Gene Names: fabI
EC: 1.3.1.39
Find proteins for A0A0H3JLH9 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  A0A0H3JLH9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
GLU
Query on GLU

Download SDF File 
Download CCD File 
A, B, C, E, F, G
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
MJ5
Query on MJ5

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
5-methyl-2-phenoxyphenol
C13 H12 O2
HUPPMDCSGSHZHI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MJ5Ki: 0.4 - 494 nM (99) BINDINGDB
MJ5Ki: 0.38 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.138 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 89.860α = 98.17
b = 94.520β = 111.87
c = 94.830γ = 97.33
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references