5I86

Crystal structure of the bromodomain of human CREBBP bound to the benzodiazepinone G02778174


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    5I8B, 5I86, 5I89, 5I83, 5I8G

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CREB-binding proteinA, B118Homo sapiensMutation(s): 0 
Gene Names: CREBBPCBP
EC: 2.3.1.48 (UniProt), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens)
Explore Q92793 
Go to UniProtKB:  Q92793
PHAROS:  Q92793
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
69A (Subject of Investigation/LOI)
Query on 69A

Download Ideal Coordinates CCD File 
E [auth A], G [auth B](4R)-N-benzyl-4-methyl-2-oxo-2,3,4,5-tetrahydro-1H-1,5-benzodiazepine-6-carboxamide
C18 H19 N3 O2
NUBAPEXWNUTLEU-GFCCVEGCSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

Download Ideal Coordinates CCD File 
D [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
69A Binding MOAD:  5I86 IC50: 530 (nM) from 1 assay(s)
BindingDB:  5I86 IC50: 530 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.993α = 96.77
b = 42.002β = 109.7
c = 49.8γ = 99.39
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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