5S9O

CRYSTAL STRUCTURE OF THE HUMAN BRD2 BD1 BROMODOMAIN IN COMPLEX WITH 9-(cyclopropylmethyl)-7-[(2R,6S)-2,6-dimethylmorpholine-4-carbonyl]-3-(3,5-dimethyl-1,2-oxazol-4-yl)-9H-carbazole-1-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery and Preclinical Pharmacology of an Oral Bromodomain and Extra-Terminal (BET) Inhibitor Using Scaffold-Hopping and Structure-Guided Drug Design.

Gavai, A.V.Norris, D.Delucca, G.Tortolani, D.Tokarski, J.S.Dodd, D.O'Malley, D.Zhao, Y.Quesnelle, C.Gill, P.Vaccaro, W.Huynh, T.Ahuja, V.Han, W.C.Mussari, C.Harikrishnan, L.Kamau, M.Poss, M.Sheriff, S.Yan, C.Marsilio, F.Menard, K.Wen, M.L.Rampulla, R.Wu, D.R.Li, J.Zhang, H.Li, P.Sun, D.Yip, H.Traeger, S.C.Zhang, Y.Mathur, A.Zhang, H.Huang, C.Yang, Z.Ranasinghe, A.Everlof, G.Raghavan, N.Tye, C.K.Wee, S.Hunt, J.T.Vite, G.Westhouse, R.Lee, F.Y.

(2021) J Med Chem 64: 14247-14265

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00625
  • Primary Citation of Related Structures:  
    5S9O, 5S9P, 5S9Q, 5S9R

  • PubMed Abstract: 

    Inhibition of the bromodomain and extra-terminal (BET) family of adaptor proteins is an attractive strategy for targeting transcriptional regulation of key oncogenes, such as c-MYC. Starting with the screening hit 1 , a combination of structure-activity relationship and protein structure-guided drug design led to the discovery of a differently oriented carbazole 9 with favorable binding to the tryptophan, proline, and phenylalanine (WPF) shelf conserved in the BET family. Identification of an additional lipophilic pocket and functional group optimization to optimize pharmacokinetic (PK) properties culminated in the discovery of 18 (BMS-986158) with excellent potency in binding and functional assays. On the basis of its favorable PK profile and robust in vivo activity in a panel of hematologic and solid tumor models, BMS-986158 was selected as a candidate for clinical evaluation.


  • Organizational Affiliation

    Research and Development, Bristol Myers Squibb Company, P. O. Box 4000, Princeton, New Jersey 08543-4000, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 2
A, B
144Homo sapiensMutation(s): 0 
Gene Names: BRD2
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
PHAROS:  P25440
GTEx:  ENSG00000204256 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25440
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YW1 (Subject of Investigation/LOI)
Query on YW1

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
9-(cyclopropylmethyl)-7-[(2R,6S)-2,6-dimethylmorpholine-4-carbonyl]-3-(3,5-dimethyl-1,2-oxazol-4-yl)-9H-carbazole-1-carboxamide
C29 H32 N4 O4
JXLZXVRZRJJOGR-IYBDPMFKSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.27α = 90
b = 134.27β = 90
c = 134.27γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2021-09-29 
  • Deposition Author(s): Sheriff, S.

Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection