5I8B | pdb_00005i8b

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: 1.52 Å
  • R-Value Free: 
    0.200 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5I8B

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acsmedchemlett.6b00075
  • Primary Citation Related Structures: 
    5I83, 5I86, 5I89, 5I8B, 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. 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.

Macromolecule Content 

  • Total Structure Weight: 32.5 kDa 
  • Atom Count: 2,207 
  • Modeled Residue Count: 226 
  • Deposited Residue Count: 264 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CREB-binding protein264Homo sapiensMutation(s): 0 
Gene Names: CREBBPCBP
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens)
Explore Q92793 
Go to UniProtKB:  Q92793
PHAROS:  Q92793
GTEx:  ENSG00000005339 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92793
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
69F

Query on 69F



Download:Ideal Coordinates CCD File
E [auth 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
B3P

Query on B3P



Download:Ideal Coordinates CCD File
F [auth A]2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
M [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
L [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free:  0.200 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.236α = 90
b = 60.576β = 102.75
c = 54.138γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

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
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations