4APP

Crystal Structure of the Human p21-Activated Kinase 4 in Complex with (S)-N-(5-(3-benzyl-1-methylpiperazine-4-carbonyl)-6,6-dimethyl-1,4,5, 6-tetrahydropyrrolo(3,4-c)pyrazol-3-yl)-3-phenoxybenzamide

• PDB DOI: https://doi.org/10.2210/pdb4APP/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-04 Released: 2012-06-06 
• Deposition Author(s): Knighton, D.D., Deng, Y.L., Wang, C., Guo, C., McAlpine, I., Zhang, J., Kephart, S., Johnson, M.C., Li, H., Bouzida, D., Yang, A., Dong, L., Marakovits, J., Tikhe, J., Richardson, P., Guo, L.C., Kania, R., Edwards, M.P., Kraynov, E., Christensen, J., Piraino, J., Lee, J., Dagostino, E., Del-Carmen, C., Smeal, T., Murray, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.229 
• R-Value Work: 0.188 

Literature

Discovery of Pyrroloaminopyrazoles as Novel Pak Inhibitors.

Guo, C., Mcalpine, I., Zhang, J., Knighton, D.D., Kephart, S., Johnson, M.C., Li, H., Bouzida, D., Yang, A., Dong, L., Marakovits, J., Tikhe, J., Richardson, P., Guo, L.C., Kania, R., Edwards, M.P., Kraynov, E., Christensen, J., Piraino, J., Lee, J., Dagostino, E., Del-Carmen, C., Deng, Y.L., Smeal, T., Murray, B.W.

(2012) J Med Chem 55: 4728

• PubMed: 22554206 
• DOI: https://doi.org/10.1021/jm300204j
• Primary Citation of Related Structures:  
  4APP


• PubMed Abstract: 
  

  The P21-activated kinases (PAK) are emerging antitumor therapeutic targets. In this paper, we describe the discovery of potent PAK inhibitors guided by structure-based drug design. In addition, the efflux of the pyrrolopyrazole series was effectively reduced by applying multiple medicinal chemistry strategies, leading to a series of PAK inhibitors that are orally active in inhibiting tumor growth in vivo.

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Organizational Affiliation: 

Pfizer Global Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States. [e-mail]

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: 34.08 kDa 
• Atom Count: 2,542 
• Modelled Residue Count: 293 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE PAK 4	A	296	Homo sapiens	Mutation(s): 0  EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O96013 (Homo sapiens) Explore O96013  Go to UniProtKB:  O96013
PHAROS:  O96013 GTEx:  ENSG00000130669

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N53	B [auth A]	N-[6,6-dimethyl-5-[(2S)-4-methyl-2-(phenylmethyl)piperazin-1-yl]carbonyl-2,4-dihydropyrrolo[3,4-c]pyrazol-3-yl]-3-phenoxy-benzamide C33 H36 N6 O3 VGRHRLOVUZTBHT-VWLOTQADSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
N53	BindingDB:  4APP	Ki: 64 (nM) from 1 assay(s)
		EC50: 810 (nM) from 1 assay(s)
	PDBBind:  4APP	Ki: 64 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.229 
• R-Value Work: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.424	α = 90
b = 64.995	β = 90
c = 85.829	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Knighton, D.D., Deng, Y.L., Wang, C., Guo, C., McAlpine, I., Zhang, J., Kephart, S., Johnson, M.C., Li, H., Bouzida, D., Yang, A., Dong, L., Marakovits, J., Tikhe, J., Richardson, P., Guo, L.C., Kania, R., Edwards, M.P., Kraynov, E., Christensen, J., Piraino, J., Lee, J., Dagostino, E., Del-Carmen, C., Smeal, T., Murray, B.W.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary