5I8B

CBP in complex with Cpd23 ((R)-6-(3-(benzyloxy)phenyl)-4-methyl-1,3,4,5-tetrahydro-2H-benzo[b][1,4]diazepin-2-one)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5218 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment-Based Discovery of a Selective and Cell-Active Benzodiazepinone CBP/EP300 Bromodomain Inhibitor (CPI-637).

Taylor, A.M.Cote, A.Hewitt, M.C.Pastor, R.Leblanc, Y.Nasveschuk, C.G.Romero, F.A.Crawford, T.D.Cantone, N.Jayaram, H.Setser, J.Murray, J.Beresini, M.H.de Leon Boenig, G.Chen, Z.Conery, A.R.Cummings, R.T.Dakin, L.A.Flynn, E.M.Huang, O.W.Kaufman, S.Keller, P.J.Kiefer, J.R.Lai, T.Li, Y.Liao, J.Liu, W.Lu, H.Pardo, E.Tsui, V.Wang, J.Wang, Y.Xu, Z.Yan, F.Yu, D.Zawadzke, L.Zhu, X.Zhu, X.Sims, R.J.Cochran, A.G.Bellon, S.Audia, J.E.Magnuson, S.Albrecht, B.K.

(2016) Acs Med.Chem.Lett. 7: 531-536

  • DOI: 10.1021/acsmedchemlett.6b00075
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CBP and EP300 are highly homologous, bromodomain-containing transcription coactivators involved in numerous cellular pathways relevant to oncology. As part of our effort to explore the potential therapeutic implications of selectively targeting bromo ...

    CBP and EP300 are highly homologous, bromodomain-containing transcription coactivators involved in numerous cellular pathways relevant to oncology. As part of our effort to explore the potential therapeutic implications of selectively targeting bromodomains, we set out to identify a CBP/EP300 bromodomain inhibitor that was potent both in vitro and in cellular target engagement assays and was selective over the other members of the bromodomain family. Reported here is a series of cell-potent and selective probes of the CBP/EP300 bromodomains, derived from the fragment screening hit 4-methyl-1,3,4,5-tetrahydro-2H-benzo[b][1,4]diazepin-2-one.


    Organizational Affiliation

    Constellation Pharmaceuticals , 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CREB-binding protein
A
264Homo sapiensMutation(s): 0 
Gene Names: CREBBP (CBP)
EC: 2.3.1.48
Find proteins for Q92793 (Homo sapiens)
Go to Gene View: CREBBP
Go to UniProtKB:  Q92793
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
B3P
Query on B3P

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Download CCD File 
A
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
69F
Query on 69F

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Download CCD File 
A
(4R)-6-[3-(benzyloxy)phenyl]-4-methyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one
C23 H22 N2 O2
XKIQUMIGIBMUJB-MRXNPFEDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
69FIC50: 110 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5218 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.236α = 90.00
b = 60.576β = 102.75
c = 54.138γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXrefinement
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-02-18 
  • Released Date: 2016-04-20 
  • Deposition Author(s): Murray, J.M.

Revision History 

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references