Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.95 kDa 
• Atom Count: 2644 
• Residue Count: 327 
• Unique protein chains: 1

4LCE

CtBP1 in complex with substrate MTOB

• DOI: 10.2210/pdb4LCE/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE SUBSTRATE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-21 Released: 2014-03-19 
• Deposition Author(s): Hilbert, B.J., Schiffer, C.A., Royer Jr., W.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.239 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

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

• PubMed: 24657618 
• DOI: 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.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-terminal-binding protein 1	A	347	Homo sapiens	Mutation(s): 0  Gene Names: CTBP, CTBP1 EC: 1.1.1
Find proteins for Q13363 (Homo sapiens) Explore Q13363  Go to UniProtKB:  Q13363
NIH Common Fund Data Resources
PHAROS:  Q13363 GTEx:  ENSG00000159692

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	A	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
KMT	A	4-(METHYLSULFANYL)-2-OXOBUTANOIC ACID C5 H8 O3 S SXFSQZDSUWACKX-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
KMT	ΔH:  14   kJ/mol  BindingDB
KMT	ΔH:  47.29999923706055   kJ/mol  BindingDB
KMT	IC50:  300000   nM  BindingDB
KMT	ΔG:  14   kJ/mol  BindingDB
KMT	-TΔS:  32.25   kJ/mol  BindingDB
KMT	Kd:  2960000   nM  BindingDB
KMT	ΔG:  16   kJ/mol  BindingDB
KMT	Kd:  1260000   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.239 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.97	α = 90
b = 88.97	β = 90
c = 161.538	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-21 
• Released Date: 2014-03-19 
Deposition Author(s): Hilbert, B.J., Schiffer, C.A., Royer Jr., W.E.

Revision History 

• 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