4ZLZ

Crystal Structure of Bruton's Tyrosine Kinase in complex with a substituted Cinnoline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Fragment-Based Discovery of a Small Molecule Inhibitor of Bruton's Tyrosine Kinase.

Smith, C.R.Dougan, D.R.Komandla, M.Kanouni, T.Knight, B.Lawson, J.D.Sabat, M.Taylor, E.R.Vu, P.Wyrick, C.

(2015) J Med Chem 58: 5437-5444

  • DOI: 10.1021/acs.jmedchem.5b00734
  • Primary Citation of Related Structures:  
    4Z3V, 4ZLY, 4ZLZ

  • PubMed Abstract: 
  • The discovery and optimization of a series of 4-aminocinnoline-3-carboxamide inhibitors of Bruton's tyrosine kinase are reported. A fragment-based screening approach incorporating X-ray co-crystallography was used to identify a cinnoline fragment and characterize its binding mode in the ATP binding site of Btk ...

    The discovery and optimization of a series of 4-aminocinnoline-3-carboxamide inhibitors of Bruton's tyrosine kinase are reported. A fragment-based screening approach incorporating X-ray co-crystallography was used to identify a cinnoline fragment and characterize its binding mode in the ATP binding site of Btk. Optimization of the fragment hit resulted in the identification of a lead compound which reduced paw swelling in a dose- and exposure-dependent fashion in a rat model of collagen-induced arthritis.


    Organizational Affiliation

    Takeda California, 10410 Science Center Drive, San Diego, California 92121, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTKA270Homo 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
4RV
Query on 4RV

Download Ideal Coordinates CCD File 
F [auth A]4-amino-8-(4-methylpyridin-3-yl)cinnoline-3-carboxamide
C15 H13 N5 O
YHEHDRMGAHEUOQ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
B [auth A],
D [auth A]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
C [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4RV Binding MOAD:  4ZLZ IC50: 100 (nM) from 1 assay(s)
BindingDB:  4ZLZ IC50: 1.00e+5 (nM) from 1 assay(s)
EC50: 2.86e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.909α = 90
b = 103.788β = 90
c = 38.032γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2015-05-01 
  • Released Date: 2015-07-01 
  • Deposition Author(s): Dougan, D.R.

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references, Other