2UW3

Structure of PKA-PKB chimera complexed with 5-methyl-4-phenyl-1H- pyrazole

• PDB DOI: https://doi.org/10.2210/pdb2UW3/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Bos taurus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-03-19 Released: 2007-05-08 
• Deposition Author(s): Davies, T.G., Saxty, G., Woodhead, S.J., Berdini, V., Verdonk, M.L., Wyatt, P.G., Boyle, R.G., Barford, D., Downham, R., Garrett, M.D., Carr, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.252 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Identification of Inhibitors of Protein Kinase B Using Fragment-Based Lead Discovery

Saxty, G., Woodhead, S.J., Berdini, V., Davies, T.G., Verdonk, M.L., Wyatt, P.G., Boyle, R.G., Barford, D., Downham, R., Garrett, M.D., Carr, R.A.

(2007) J Med Chem 50: 2293

• PubMed: 17451234 
• DOI: https://doi.org/10.1021/jm070091b
• Primary Citation of Related Structures:  
  2UW3, 2UW4, 2UW5, 2UW6, 2UW7, 2UW8, 2UW9


• PubMed Abstract: 
  

  Using fragment-based screening techniques, 5-methyl-4-phenyl-1H-pyrazole (IC50 80 microM) was identified as a novel, low molecular weight inhibitor of protein kinase B (PKB). Herein we describe the rapid elaboration of highly potent and ligand efficient analogues using a fragment growing approach. Iterative structure-based design was supported by protein-ligand structure determinations using a PKA-PKB "chimera" and a final protein-ligand structure of a lead compound in PKBbeta itself.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 43.3 kDa 
• Atom Count: 3,200 
• Modelled Residue Count: 357 
• Deposited Residue Count: 371 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT	A	351	Bos taurus	Mutation(s): 4  EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus) Explore P00517  Go to UniProtKB:  P00517

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA	B [auth I]	20	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens) Explore P61925  Go to UniProtKB:  P61925
PHAROS:  P61925 GTEx:  ENSG00000171033

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GVG	C [auth A]	3-METHYL-4-PHENYL-1H-PYRAZOLE C10 H10 N2 XTXZCNATVCIKTR-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.252 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.789	α = 90
b = 74.49	β = 90
c = 79.711	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-08 
Deposition Author(s): Davies, T.G., Saxty, G., Woodhead, S.J., Berdini, V., Verdonk, M.L., Wyatt, P.G., Boyle, R.G., Barford, D., Downham, R., Garrett, M.D., Carr, R.A.

Revision History  

• Version 1.0: 2007-05-08
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary