5I40

BRD9 in complex with Cpd1 (6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains.

Crawford, T.D.Tsui, V.Flynn, E.M.Wang, S.Taylor, A.M.Cote, A.Audia, J.E.Beresini, M.H.Burdick, D.J.Cummings, R.Dakin, L.A.Duplessis, M.Good, A.C.Hewitt, M.C.Huang, H.R.Jayaram, H.Kiefer, J.R.Jiang, Y.Murray, J.Nasveschuk, C.G.Pardo, E.Poy, F.Romero, F.A.Tang, Y.Wang, J.Xu, Z.Zawadzke, L.E.Zhu, X.Albrecht, B.K.Magnuson, S.R.Bellon, S.Cochran, A.G.

(2016) J Med Chem 59: 5391-5402

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00264
  • Primary Citation of Related Structures:  
    5I1Q, 5I29, 5I40, 5I7X, 5I7Y, 5I80, 5I88

  • PubMed Abstract: 

    The biological role played by non-BET bromodomains remains poorly understood, and it is therefore imperative to identify potent and highly selective inhibitors to effectively explore the biology of individual bromodomain proteins. A ligand-efficient nonselective bromodomain inhibitor was identified from a 6-methyl pyrrolopyridone fragment. Small hydrophobic substituents replacing the N-methyl group were designed directing toward the conserved bromodomain water pocket, and two distinct binding conformations were then observed. The substituents either directly displaced and rearranged the conserved solvent network, as in BRD4(1) and TAF1(2), or induced a narrow hydrophobic channel adjacent to the lipophilic shelf, as in BRD9 and CECR2. The preference of distinct substituents for individual bromodomains provided selectivity handles useful for future lead optimization efforts for selective BRD9, CECR2, and TAF1(2) inhibitors.


  • Organizational Affiliation

    Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 9102Homo sapiensMutation(s): 0 
Gene Names: BRD9UNQ3040/PRO9856
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H8M2 (Homo sapiens)
Explore Q9H8M2 
Go to UniProtKB:  Q9H8M2
PHAROS:  Q9H8M2
GTEx:  ENSG00000028310 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H8M2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
67N
Query on 67N

Download Ideal Coordinates CCD File 
G [auth A]6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one
C8 H8 N2 O
ZLKWLYKVKAVOMD-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
67N BindingDB:  5I40 IC50: 1.37e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.58α = 70.47
b = 33.745β = 73.32
c = 39.503γ = 74.52
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2016-10-12 
  • Deposition Author(s): Murray, J.M.

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations