CtBP1 bound to inhibitor 2-(hydroxyimino)-3-phenylpropanoic acid

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structure-Guided Design of a High Affinity Inhibitor to Human CtBP.

Hilbert, B.J.Morris, B.L.Ellis, K.C.Paulsen, J.L.Schiffer, C.A.Grossman, S.R.Royer, W.E.

(2015) ACS Chem Biol 10: 1118-1127

  • DOI: https://doi.org/10.1021/cb500820b
  • Primary Citation of Related Structures:  
    4U6Q, 4U6S

  • PubMed Abstract: 

    Oncogenic transcriptional coregulators C-terminal Binding Protein (CtBP) 1 and 2 possess regulatory d-isomer specific 2-hydroxyacid dehydrogenase (D2-HDH) domains that provide an attractive target for small molecule intervention. Findings that the CtBP substrate 4-methylthio 2-oxobutyric acid (MTOB) can interfere with CtBP oncogenic activity in cell culture and in mice confirm that such inhibitors could have therapeutic benefit. Recent crystal structures of CtBP 1 and 2 revealed that MTOB binds in an active site containing a dominant tryptophan and a hydrophilic cavity, neither of which are present in other D2-HDH family members. Here, we demonstrate the effectiveness of exploiting these active site features for the design of high affinity inhibitors. Crystal structures of two such compounds, phenylpyruvate (PPy) and 2-hydroxyimino-3-phenylpropanoic acid (HIPP), show binding with favorable ring stacking against the CtBP active site tryptophan and alternate modes of stabilizing the carboxylic acid moiety. Moreover, ITC experiments show that HIPP binds to CtBP with an affinity greater than 1000-fold over that of MTOB, and enzymatic assays confirm that HIPP substantially inhibits CtBP catalysis. These results, thus, provide an important step, and additional insights, for the development of highly selective antineoplastic CtBP inhibitors.

  • Organizational Affiliation

    †Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-terminal-binding protein 1347Homo sapiensMutation(s): 0 
Gene Names: CTBP1CTBP
EC: 1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13363 (Homo sapiens)
Explore Q13363 
Go to UniProtKB:  Q13363
PHAROS:  Q13363
GTEx:  ENSG00000159692 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13363
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
3CR BindingDB:  4U6Q Kd: min: 370, max: 2770 (nM) from 3 assay(s)
IC50: 745 (nM) from 1 assay(s)
-TΔS: min: 8.79, max: 35.18 (kJ/mol) from 3 assay(s)
ΔH: min: -6.99e+1, max: -4.19e+1 (kJ/mol) from 3 assay(s)
ΔG: min: -3.60e+1, max: -3.10e+1 (kJ/mol) from 3 assay(s)
Binding MOAD:  4U6Q Kd: 370 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84α = 90
b = 84β = 90
c = 159.472γ = 120
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy