A very short hydrogen bond provides only moderate stabilization of an enzyme: inhibitor complex of citrate synthase

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Observed: 0.156 

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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: 7753-7759

  • DOI: https://doi.org/10.1021/bi00191a002
  • Primary Citation of Related Structures:  
    1CSH, 1CSI

  • PubMed Abstract: 

    Two extremely potent inhibitors of citrate synthase, carboxyl and primary amide analogues of acetyl coenzyme A, have been synthesized. The ternary complexes of these inhibitors with oxaloacetate and citrate synthase have been crystallized and their structures analyzed at 1.70- and 1.65-A resolution, respectively. The inhibitors have dissociation constants in the nanomolar range, with the carboxyl analogue binding more tightly (Ki = 1.6 nM at pH 6.0) than the amide analogue (28 nM), despite the unfavorable requirement for proton uptake by the former. The carboxyl group forms a shorter hydrogen bond with the catalytic Asp 375 (distance < 2.4 A) than does the amide group (distance approximately 2.5 A). Particularly with the carboxylate inhibitor, the very short hydrogen bond distances measured suggest a low barrier or short strong hydrogen bond. However, the binding constants differ by only a factor of 20 at pH 6.0, corresponding to an increase in binding energy for the carboxyl analogue on the enzyme of about 2 kcal/mol more than the amide analogue, much less than has been proposed for short strong hydrogen bonds based on gas phase measurements [> 20 kcal/mol (Gerlt & Gassman, 1993a,b)]. The inhibitor complexes support proposals that Asp 375 and His 274 work in concert to form an enolized form of acetyl-coenzyme A as the first step in the reaction.

  • Organizational Affiliation

    Institute of Molecular Biology, University of Oregon, Eugene 97403.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CITRATE SYNTHASE435Gallus gallusMutation(s): 0 
Find proteins for P23007 (Gallus gallus)
Explore P23007 
Go to UniProtKB:  P23007
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23007
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CMX

Download Ideal Coordinates CCD File 
C23 H38 N7 O18 P3
Query on OAA

Download Ideal Coordinates CCD File 
C4 H3 O5
Binding Affinity Annotations 
IDSourceBinding Affinity
CMX PDBBind:  1CSI Ki: 1.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Observed: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.4α = 90
b = 78.5β = 78.9
c = 58.5γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-04-30
    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
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations