4U6Q

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-terminal-binding protein 1A347Homo sapiensMutation(s): 0 
Gene Names: CTBP1CTBP
EC: 1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13363 (Homo sapiens)
Explore Q13363 
Go to UniProtKB:  Q13363
PHAROS:  Q13363
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download Ideal Coordinates CCD File 
B [auth A]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
3CR
Query on 3CR

Download Ideal Coordinates CCD File 
C [auth A](2E)-2-(hydroxyimino)-3-phenylpropanoic acid
C9 H9 N O3
PNTMGOUAICFJQK-CSKARUKUSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
E [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3CR-TΔS:  8.789999961853027   kJ/mol  BindingDB
3CR-TΔS:  35.18000030517578   kJ/mol  BindingDB
3CRKd:  370   nM  Binding MOAD
3CRIC50:  745   nM  BindingDB
3CRKd:  370   nM  BindingDB
3CRΔG:  31   kJ/mol  BindingDB
3CRΔH:  69.9000015258789   kJ/mol  BindingDB
3CRΔG:  36   kJ/mol  BindingDB
3CRΔG:  33   kJ/mol  BindingDB
3CRΔH:  41.900001525878906   kJ/mol  BindingDB
3CRKd:  1300   nM  BindingDB
3CR-TΔS:  16.1200008392334   kJ/mol  BindingDB
3CRΔH:  47.70000076293945   kJ/mol  BindingDB
3CRKd:  2770   nM  BindingDB
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 = 84α = 90
b = 84β = 90
c = 159.472γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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