3KCF

Crystal structure of TGFbRI complexed with a pyrazolone inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Pyrazolone based TGFbetaR1 kinase inhibitors.

Guckian, K., Carter, M.B., Lin, E.Y., Choi, M., Sun, L., Boriack-Sjodin, P.A., Chuaqui, C., Lane, B., Cheung, K., Ling, L., Lee, W.C.

(2010) Bioorg Med Chem Lett 20: 326-329

  • DOI: 10.1016/j.bmcl.2009.10.108
  • Primary Citation of Related Structures:  
    3KCF

  • PubMed Abstract: 

    • Interruption of TGFbeta signaling through inhibition of the TGFbetaR1 kinase domain may prove to have beneficial effect in both fibrotic and oncological diseases. Herein we describe the SAR of a novel series of TGFbetaR1 kinase inhibitors containing a pyrazolone core ...

    Interruption of TGFbeta signaling through inhibition of the TGFbetaR1 kinase domain may prove to have beneficial effect in both fibrotic and oncological diseases. Herein we describe the SAR of a novel series of TGFbetaR1 kinase inhibitors containing a pyrazolone core. Most TGFbetaR1 kinase inhibitors described to date contain a core five-membered ring bearing N as H-bond acceptor. Described herein is a novel strategy to replace the core structure with pyrazolone ring, in which the carbonyl group is designed as an H-bond acceptor to interact with catalytic Lys 232.

    Organizational Affiliation: 

    Biogen Idec Inc., 14 Cambridge Center, Cambridge, MA 02142, USA. kevin.guckian@biogenidec.com



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TGF-beta receptor type-1A, B, C, D, E342Homo sapiensMutation(s): 0 
Gene Names: TGFBR1, TGFBRI, ALK5, SKR4
EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P36897 (Homo sapiens)
Explore P36897 
Go to UniProtKB:  P36897
PHAROS:  P36897
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36897
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JZO
Query on JZO
Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C],
P [auth D],
T [auth E]		4-[3-(methoxymethyl)phenyl]-1,2-dimethyl-5-quinoxalin-6-yl-1,2-dihydro-3H-pyrazol-3-one
C21 H20 N4 O2
OWJLLMXRMBEWIM-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
Q [auth D],
R [auth D],
S [auth D],
U [auth E],
V [auth E],
W [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
JZO BindingDB:  3KCF Ki: 35 (nM) from 1 assay(s)
IC50: 3690 (nM) from 1 assay(s)
PDBBind:  3KCF Ki: 35 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.025α = 90
b = 249.076β = 90
c = 138.011γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2009-10-21 
  • Released Date: 2009-12-22 
    • Deposition Author(s): Boriack-Sjodin, P.A.

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance