3IW4 | pdb_00003iw4

Crystal structure of PKC alpha in complex with NVP-AEB071

• PDB DOI: https://doi.org/10.2210/pdb3IW4/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2009-09-02 Released: 2009-11-03 
• Deposition Author(s): Stark, W., Rummel, G., Strauss, A., Cowan-Jacob, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Discovery of 3-(1H-indol-3-yl)-4-[2-(4-methylpiperazin-1-yl)quinazolin-4-yl]pyrrole-2,5-dione (AEB071), a potent and selective inhibitor of protein kinase C isotypes

Wagner, J., von Matt, P., Sedrani, R., Albert, R., Cooke, N., Ehrhardt, C., Geiser, M., Rummel, G., Stark, W., Strauss, A., Cowan-Jacob, S.W., Beerli, C., Weckbecker, G., Evenou, J.P., Zenke, G., Cottens, S.

(2009) J Med Chem 52: 6193-6196

• PubMed: 19827831 
• DOI: https://doi.org/10.1021/jm901108b
• Primary Citation of Related Structures:  
  3IW4


• PubMed Abstract: 
  

  A series of novel maleimide-based inhibitors of protein kinase C (PKC) were designed, synthesized, and evaluated. AEB071 (1) was found to be a potent, selective inhibitor of classical and novel PKC isotypes. 1 is a highly efficient immunomodulator, acting via inhibition of early T cell activation. The binding mode of maleimides to PKCs, proposed by molecular modeling, was confirmed by X-ray analysis of 1 bound in the active site of PKCalpha.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 126.03 kDa 
• Atom Count: 8,196 
• Modelled Residue Count: 993 
• Deposited Residue Count: 1,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein kinase C alpha type	A, B, C	360	Homo sapiens	Mutation(s): 1  Gene Names: PRKCA, PKCA, PRKACA EC: 2.7.11.13
UniProt & NIH Common Fund Data Resources
Find proteins for P17252 (Homo sapiens) Explore P17252  Go to UniProtKB:  P17252
PHAROS:  P17252 GTEx:  ENSG00000154229

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LW4	D [auth A], E [auth B], F [auth C]	3-(1H-indol-3-yl)-4-[2-(4-methylpiperazin-1-yl)quinazolin-4-yl]-1H-pyrrole-2,5-dione C25 H22 N6 O2 OAVGBZOFDPFGPJ-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
LW4	BindingDB:  3IW4	IC50: min: 0.95, max: 2.1 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.868	α = 90
b = 100.669	β = 90
c = 251.335	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Stark, W., Rummel, G., Strauss, A., Cowan-Jacob, S.W.

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary