CtBP2 in complex with substrate MTOB

Experimental Data Snapshot

  • Resolution: 2.86 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 

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Crystal structures of human CtBP in complex with substrate MTOB reveal active site features useful for inhibitor design.

Hilbert, B.J.Grossmann, S.R.Schiffer, C.A.Royer, W.E.

(2014) FEBS Lett 588: 1743-1748

  • DOI: https://doi.org/10.1016/j.febslet.2014.03.026
  • Primary Citation of Related Structures:  
    4LCE, 4LCJ

  • PubMed Abstract: 

    The oncogenic corepressors C-terminal Binding Protein (CtBP) 1 and 2 harbor regulatory d-isomer specific 2-hydroxyacid dehydrogenase (d2-HDH) domains. 4-Methylthio 2-oxobutyric acid (MTOB) exhibits substrate inhibition and can interfere with CtBP oncogenic activity in cell culture and mice. Crystal structures of human CtBP1 and CtBP2 in complex with MTOB and NAD(+) revealed two key features: a conserved tryptophan that likely contributes to substrate specificity and a hydrophilic cavity that links MTOB with an NAD(+) phosphate. Neither feature is present in other d2-HDH enzymes. These structures thus offer key opportunities for the development of highly selective anti-neoplastic CtBP inhibitors.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-terminal-binding protein 2
A, B, C, D, E
A, B, C, D, E, F, G, H
349Homo sapiensMutation(s): 0 
Gene Names: CTBP2
UniProt & NIH Common Fund Data Resources
Find proteins for P56545 (Homo sapiens)
Explore P56545 
Go to UniProtKB:  P56545
PHAROS:  P56545
GTEx:  ENSG00000175029 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56545
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G],
W [auth H]
C21 H27 N7 O14 P2
Query on KMT

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G],
X [auth H]
C5 H8 O3 S
Binding Affinity Annotations 
IDSourceBinding Affinity
KMT BindingDB:  4LCJ Kd: min: 1.26e+6, max: 2.96e+6 (nM) from 2 assay(s)
IC50: 3.00e+5 (nM) from 1 assay(s)
-TΔS: 32.25 (kJ/mol) from 1 assay(s)
ΔH: min: -4.73e+1, max: -1.40e+1 (kJ/mol) from 2 assay(s)
ΔG: min: -1.60e+1, max: -1.40e+1 (kJ/mol) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.86 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.151α = 90
b = 140.605β = 97.87
c = 135.126γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-04-09
    Changes: Database references
  • Version 1.2: 2014-05-14
    Changes: Database references
  • Version 1.3: 2014-11-12
    Changes: Structure summary
  • Version 1.4: 2017-11-15
    Changes: Refinement description
  • Version 1.5: 2024-02-28
    Changes: Data collection, Database references, Derived calculations