Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 39.07 kDa 
• Atom Count: 2688 
• Modelled Residue Count: 328 
• Deposited Residue Count: 347 
• Unique protein chains: 1

4U6Q

CtBP1 bound to inhibitor 2-(hydroxyimino)-3-phenylpropanoic acid

• PDB DOI: 10.2210/pdb4U6Q/pdb

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


• Deposited: 2014-07-29 Released: 2015-02-11 
• Deposition Author(s): Hilbert, B.J., Morris, B.L., Ellis, K.C., Paulsen, J.L., Schiffer, C.A., Grossman, S.R., Royer Jr., W.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.249 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Structure-Guided Design of a High Affinity Inhibitor to Human CtBP.

Hilbert, B.J., Morris, B.L., Ellis, K.C., Paulsen, J.L., Schiffer, C.A., Grossman, S.R., Royer, W.E.

(2015) ACS Chem Biol 10: 1118-1127

• PubMed: 25636004 
• DOI: 10.1021/cb500820b
• Primary Citation of Related Structures:  
  4U6Q, 4U6S


• PubMed Abstract: 
  

Oncogenic transcriptional coregulators C-terminal Binding Protein (CtBP) 1 and 2 possess regulatory d-isomer specific 2-hydroxyacid dehydrogenase (D2-HDH) domains that provide an attractive target for small molecule intervention. Findings that the CtBP substrate 4-methylthio 2-oxobutyric acid (MTOB) can interfere with CtBP oncogenic activity in cell culture and in mice confirm that such inhibitors could have therapeutic benefit. Recent crystal structures of CtBP 1 and 2 revealed that MTOB binds in an active site containing a dominant tryptophan and a hydrophilic cavity, neither of which are present in other D2-HDH family members. Here, we demonstrate the effectiveness of exploiting these active site features for the design of high affinity inhibitors. Crystal structures of two such compounds, phenylpyruvate (PPy) and 2-hydroxyimino-3-phenylpropanoic acid (HIPP), show binding with favorable ring stacking against the CtBP active site tryptophan and alternate modes of stabilizing the carboxylic acid moiety. Moreover, ITC experiments show that HIPP binds to CtBP with an affinity greater than 1000-fold over that of MTOB, and enzymatic assays confirm that HIPP substantially inhibits CtBP catalysis. These results, thus, provide an important step, and additional insights, for the development of highly selective antineoplastic CtBP inhibitors.

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Organizational Affiliation: 

†Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States.

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: CTBP1, CTBP EC: 1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13363 (Homo sapiens) Explore Q13363  Go to UniProtKB:  Q13363
PHAROS:  Q13363

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	B [auth A]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
3CR	C [auth A]	(2E)-2-(hydroxyimino)-3-phenylpropanoic acid C9 H9 N O3 PNTMGOUAICFJQK-CSKARUKUSA-N
FMT	E [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3CR	BindingDB:  4U6Q	Kd: min: 370, max: 2770 (nM) from 3 assay(s)
		IC50: 745 (nM) from 1 assay(s)
		-TΔS: min: 8.79, max: 35.18 (kJ/mol) from 3 assay(s)
		ΔH: min: -6.99e+1, max: -4.19e+1 (kJ/mol) from 3 assay(s)
		ΔG: min: -3.60e+1, max: -3.10e+1 (kJ/mol) from 3 assay(s)
	Binding MOAD:  4U6Q	Kd: 370 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.249 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84	α = 90
b = 84	β = 90
c = 159.472	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-07-29 
• Released Date: 2015-02-11 
Deposition Author(s): Hilbert, B.J., Morris, B.L., Ellis, K.C., Paulsen, J.L., Schiffer, C.A., Grossman, S.R., Royer Jr., W.E.

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Database references