4LCJ

CtBP2 in complex with substrate MTOB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: 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

    Division of Hematology, Oncology, and Palliative Care and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA.


Macromolecules
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
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]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
KMT
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]
4-(METHYLSULFANYL)-2-OXOBUTANOIC ACID
C5 H8 O3 S
SXFSQZDSUWACKX-UHFFFAOYSA-N
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

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



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