Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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: 38951.07 
• Atom Count: 2560 
• Residue Count: 347 
• 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)


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

---

Experimental Data Snapshot

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

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:  
  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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
C-terminal-binding protein 1	A	347	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
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 - -47.3 kJ/mol (100) BINDINGDB
KMT	ΔG: -14 - -16 kJ/mol (100) BINDINGDB
KMT	IC50: 300000 nM (88) BINDINGDB
KMT	Kd: 1260000 - 2960000 nM (100) BINDINGDB

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 = 88.970	α = 90.00
b = 88.970	β = 90.00
c = 161.538	γ = 120.00

Software Package:

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