1CSR

Alpha-fluoro acid and alpha-fluoro amide analogs of acetyl-coa as inhibitors of of citrate synthase: effect of pka matching on binding affinity and hydrogen bond length


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

alpha-Fluoro acid and alpha-fluoro amide analogs of acetyl-CoA as inhibitors of citrate synthase: effect of pKa matching on binding affinity and hydrogen bond length.

Schwartz, B.Drueckhammer, D.G.Usher, K.C.Remington, S.J.

(1995) Biochemistry 34: 15459-15466

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An alpha-fluoro acid analog and an alpha-fluoro amide analog of acetyl-CoA have been synthesized. The ternary complexes of these inhibitors with oxaloacetate and citrate synthase have been crystallized and their structures analyzed at 1.7 A resolutio ...

    An alpha-fluoro acid analog and an alpha-fluoro amide analog of acetyl-CoA have been synthesized. The ternary complexes of these inhibitors with oxaloacetate and citrate synthase have been crystallized and their structures analyzed at 1.7 A resolution. The structures are similar to those reported for the corresponding non-fluorinated analogs (Usher et al., 1994), with all forming unusually short hydrogen bonds to Asp 375. The alpha-fluoro amide analog binds with an affinity 1.5-fold lower than that of a previously described amide analog lacking the alpha-fluoro group. The alpha-fluoro acid analog binds with a 50-fold decreased affinity relative to the corresponding unfluorinated analog. The binding affinities are consistent with increased strengths of hydrogen bonds to Asp 375 with closer matching of pKa values between hydrogen bond donors and acceptors. The results do not support any direct correlation between hydrogen bond strength and hydrogen bond length in enzyme-inhibitor complexes.


    Related Citations: 
    • Proposed Mechanism for the Condensation Reaction of Citrate Synthase: 1.9-Angstroms Structure of the Ternary Complex with Oxaloacetate and Carboxymethyl Coenzyme A
      Karpusas, M.,Branchaud, B.,Remington, S.J.
      (1990) Biochemistry 29: 2213
    • Crystallographic Refinement and Atomic Models of Two Different Forms of Citrate Synthase at 2.7 And 1.7 Angstroms Resolution
      Remington, S.,Wiegand, G.,Huber, R.
      (1982) J.Mol.Biol. 158: 111
    • A Very Short Hydrogen Bond Provides Only Moderate Stabilization of an Enzyme-Inhibitor Complex of Citrate Synthase
      Usher, K.C.,Remington, S.J.,Martin, D.P.,Drueckhammer, D.G.
      (1994) Biochemistry 33: 7753
    • Crystal Structure Analysis and Molecular Model of a Complex of Citrate Synthase with Oxaloacetate and S-Acetonyl-Coenzyme A
      Wiegand, G.,Remington, S.,Deisenhofer, J.,Huber, R.
      (1984) J.Mol.Biol. 174: 205


    Organizational Affiliation

    Department of Chemistry, Stanford University, California 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CITRATE SYNTHASE
A
435Gallus gallusMutation(s): 0 
Gene Names: CS
EC: 2.3.3.1
Find proteins for P23007 (Gallus gallus)
Go to Gene View: CS
Go to UniProtKB:  P23007
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAM
Query on FAM

Download SDF File 
Download CCD File 
A
ALPHA-FLUORO-AMIDOCARBOXYMETHYLDETHIA COENZYME A COMPLEX
C23 H38 F N8 O17 P3
AXBPCHJFKHSRQL-SYSIYMLXSA-N
 Ligand Interaction
OAA
Query on OAA

Download SDF File 
Download CCD File 
A
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FAMKi: 42 nM BINDINGMOAD
FAMKi: 42 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.390α = 90.00
b = 78.430β = 78.86
c = 58.470γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
R-AXISdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other