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: 1.70 Å
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


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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

  • DOI: 10.1021/bi00047a010
  • Primary Citation of Related Structures:  
    1CSR, 1CSS

  • 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 resolution. The structures are similar to those reported for the corresponding non-fluorinated analogs (Usher et al ...

    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: 
    • 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
    • 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
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CITRATE SYNTHASEA435Gallus gallusMutation(s): 0 
Gene Names: CS
EC: 4.1.3.7 (PDB Primary Data), 2.3.3.1 (UniProt)
UniProt
Find proteins for P23007 (Gallus gallus)
Explore P23007 
Go to UniProtKB:  P23007
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAM (Subject of Investigation/LOI)
Query on FAM

Download Ideal Coordinates CCD File 
C [auth A]ALPHA-FLUORO-AMIDOCARBOXYMETHYLDETHIA COENZYME A COMPLEX
C23 H38 F N8 O17 P3
AXBPCHJFKHSRQL-SYSIYMLXSA-N
 Ligand Interaction
OAA
Query on OAA

Download Ideal Coordinates CCD File 
B [auth A]OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FAM PDBBind:  1CSR Ki: 42 (nM) from 1 assay(s)
Binding MOAD:  1CSR Ki: 42 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.39α = 90
b = 78.43β = 78.86
c = 58.47γ = 90
Software Package:
Software NamePurpose
TNTrefinement
R-AXISdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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