2YIY | pdb_00002yiy

Crystal structure of compound 8 bound to TAK1-TAB

• PDB DOI: https://doi.org/10.2210/pdb2YIY/pdb

• Classification: TRANSFERASE/TRANSFERASE ACTIVATOR
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2011-05-17 Released: 2012-05-23 
• Deposition Author(s): Brown, D.G., Phillips, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.245 (Depositor) 
• R-Value Work: 
  0.188 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

The Discovery and Synthesis of Selective Dfg-Out Tak-1 Inhibitors

Green, M.P., Bell, A., Bess, K., Brown, D.G., Campany, K., Dodd, P., Hewson, C., Hughes, S.J., Kilty, I., Phillips, C., Smith, R.T., Hoorn, W.V., Jones, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.23 kDa 
• Atom Count: 2,568 
• Modeled Residue Count: 293 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7, TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1	A	307	Homo sapiens	Mutation(s): 0  EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for O43318 (Homo sapiens) Explore O43318  Go to UniProtKB:  O43318
PHAROS:  O43318 GTEx:  ENSG00000135341
Find proteins for Q15750 (Homo sapiens) Explore Q15750  Go to UniProtKB:  Q15750
PHAROS:  Q15750 GTEx:  ENSG00000100324
UniProt Groups	O43318Q15750

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YIY	B [auth A]	(1E)-1-[5-TERT-BUTYL-2-(3-FLUOROPHENYL)-1H-PYRAZOL-3-YLIDENE]-3-(4-PYRIDIN-3-YLOXYPHENYL)UREA C25 H24 F N5 O2 VWGLIDHWYMNSEW-BYNJWEBRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.245 (Depositor) 
• R-Value Work:  0.188 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.401	α = 90
b = 133.422	β = 90
c = 145.769	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Brown, D.G., Phillips, C.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2019-03-27
  Changes: Data collection, Other, Source and taxonomy
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description