5VGO

Bruton's tyrosine kinase (BTK) with compound G-744


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of Potent and Selective Tricyclic Inhibitors of Bruton's Tyrosine Kinase with Improved Druglike Properties.

Wang, X.Barbosa, J.Blomgren, P.Bremer, M.C.Chen, J.Crawford, J.J.Deng, W.Dong, L.Eigenbrot, C.Gallion, S.Hau, J.Hu, H.Johnson, A.R.Katewa, A.Kropf, J.E.Lee, S.H.Liu, L.Lubach, J.W.Macaluso, J.Maciejewski, P.Mitchell, S.A.Ortwine, D.F.DiPaolo, J.Reif, K.Scheerens, H.Schmitt, A.Wong, H.Xiong, J.M.Xu, J.Zhao, Z.Zhou, F.Currie, K.S.Young, W.B.

(2017) ACS Med Chem Lett 8: 608-613

  • DOI: 10.1021/acsmedchemlett.7b00103
  • Primary Citation of Related Structures:  
    5VGO

  • PubMed Abstract: 
  • In our continued effort to discover and develop best-in-class Bruton's tyrosine kinase (Btk) inhibitors for the treatment of B-cell lymphomas, rheumatoid arthritis, and systemic lupus erythematosus, we devised a series of novel tricyclic compounds that improved upon the druglike properties of our previous chemical matter ...

    In our continued effort to discover and develop best-in-class Bruton's tyrosine kinase (Btk) inhibitors for the treatment of B-cell lymphomas, rheumatoid arthritis, and systemic lupus erythematosus, we devised a series of novel tricyclic compounds that improved upon the druglike properties of our previous chemical matter. Compounds exemplified by G-744 are highly potent, selective for Btk, metabolically stable, well tolerated, and efficacious in an animal model of arthritis.


    Organizational Affiliation

    Genentech, Inc., Research and Early Development, 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
Tyrosine-protein kinase BTKA271Homo sapiensMutation(s): 0 
Gene Names: BTKAGMX1ATKBPK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
PHAROS:  Q06187
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9B1
Query on 9B1

Download Ideal Coordinates CCD File 
H [auth A]2-[2-(hydroxymethyl)-3-{1-methyl-6-oxo-5-[(pyrimidin-4-yl)amino]-1,6-dihydropyridin-3-yl}phenyl]-6,6-dimethyl-3,4,6,7-tetrahydro-2H-cyclopenta[4,5]thieno[2,3-c]pyridin-1(5H)-one
C29 H29 N5 O3 S
QAESSIFTPVEYRY-UHFFFAOYSA-N
 Ligand Interaction
PG0
Query on PG0

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9B1 BindingDB:  5VGO Ki: 1.3 (nM) from 1 assay(s)
IC50: min: 2, max: 87 (nM) from 4 assay(s)
EC50: min: 22, max: 33 (nM) from 2 assay(s)
Binding MOAD:  5VGO Ki: 1.28 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.314α = 90
b = 108.314β = 90
c = 42.57γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2017-04-11 
  • Released Date: 2017-07-05 
  • Deposition Author(s): Yu, C., Eigenbrot, C.

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release