5W0I

CREBBP Bromodomain in complex with Cpd8 (1-(3-(7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl)-1-(tetrahydrofuran-3-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl)ethan-1-one)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

GNE-781, A Highly Advanced Potent and Selective Bromodomain Inhibitor of Cyclic Adenosine Monophosphate Response Element Binding Protein, Binding Protein (CBP).

Romero, F.A., Murray, J., Lai, K.W., Tsui, V., Albrecht, B.K., An, L., Beresini, M.H., de Leon Boenig, G., Bronner, S.M., Chan, E.W., Chen, K.X., Chen, Z., Choo, E.F., Clagg, K., Clark, K., Crawford, T.D., Cyr, P., de Almeida Nagata, D., Gascoigne, K.E., Grogan, J.L., Hatzivassiliou, G., Huang, W., Hunsaker, T.L., Kaufman, S., Koenig, S.G., Li, R., Li, Y., Liang, X., Liao, J., Liu, W., Ly, J., Maher, J., Masui, C., Merchant, M., Ran, Y., Taylor, A.M., Wai, J., Wang, F., Wei, X., Yu, D., Zhu, B.Y., Zhu, X., Magnuson, S.

(2017) J Med Chem 60: 9162-9183

  • DOI: 10.1021/acs.jmedchem.7b00796
  • Primary Citation of Related Structures:  
    5W0F, 5W0I, 5W0L, 5W0Q

  • PubMed Abstract: 

    • Inhibition of the bromodomain of the transcriptional regulator CBP/P300 is an especially interesting new therapeutic approach in oncology. We recently disclosed in vivo chemical tool 1 (GNE-272) for the bromodomain of CBP that was moderately potent and selective over BRD4(1) ...

    Inhibition of the bromodomain of the transcriptional regulator CBP/P300 is an especially interesting new therapeutic approach in oncology. We recently disclosed in vivo chemical tool 1 (GNE-272) for the bromodomain of CBP that was moderately potent and selective over BRD4(1). In pursuit of a more potent and selective CBP inhibitor, we used structure-based design. Constraining the aniline of 1 into a tetrahydroquinoline motif maintained potency and increased selectivity 2-fold. Structure-activity relationship studies coupled with further structure-based design targeting the LPF shelf, BC loop, and KAc regions allowed us to significantly increase potency and selectivity, resulting in the identification of non-CNS penetrant 19 (GNE-781, TR-FRET IC 50 = 0.94 nM, BRET IC 50 = 6.2 nM; BRD4(1) IC 50 = 5100 nΜ) that maintained good in vivo PK properties in multiple species. Compound 19 displays antitumor activity in an AML tumor model and was also shown to decrease Foxp3 transcript levels in a dose dependent manner.

    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
MoleculeChainsSequence LengthOrganismDetailsImage
CREB-binding proteinA148Mus musculusMutation(s): 0 
Gene Names: Crebbp, Cbp
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt
Find proteins for P45481 (Mus musculus)
Explore P45481 
Go to UniProtKB:  P45481
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45481
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9UA
Query on 9UA
Download Ideal Coordinates CCD File 
B [auth A]1-{3-[7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl]-1-[(3S)-oxolan-3-yl]-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl}ethan-1-one
C26 H30 F2 N6 O2
FLTYKXCCCAPRLV-IBGZPJMESA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9UA BindingDB:  5W0I IC50: min: 1.4, max: 37 (nM) from 2 assay(s)
Binding MOAD:  5W0I IC50: 1.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.879α = 90
b = 48.602β = 90
c = 80.763γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2017-05-30 
  • Released Date: 2018-03-07 
    • Deposition Author(s): Murray, J.M.

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release