4LCE

CtBP1 in complex with substrate MTOB

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

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: 10.1016/j.febslet.2014.03.026
  • Primary Citation of Related Structures:  

  • 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 onc ...

    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: 

    Division of Hematology, Oncology, and Palliative Care and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address: William.Royer@umassmed.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-terminal-binding protein 1
A
347Homo sapiensMutation(s): 0 
Gene Names: CTBP1 (CTBP)
EC: 1.1.1.-
Find proteins for Q13363 (Homo sapiens)
Go to Gene View: CTBP1
Go to UniProtKB:  Q13363
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download SDF File 
Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
KMT
Query on KMT
Download SDF File 
Download CCD File 
A
4-(METHYLSULFANYL)-2-OXOBUTANOIC ACID
C5 H8 O3 S
SXFSQZDSUWACKX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 88.970α = 90.00
b = 88.970β = 90.00
c = 161.538γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data scaling
DENZOdata reduction
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Database references
  • Version 1.2: 2014-05-14
    Type: Database references
  • Version 1.3: 2014-11-12
    Type: Structure summary
  • Version 1.4: 2017-11-15
    Type: Refinement description