4ID7 | pdb_00004id7

ACK1 kinase in complex with the inhibitor cis-3-[8-amino-1-(4-phenoxyphenyl)imidazo[1,5-a]pyrazin-3-yl]cyclobutanol

• PDB DOI: https://doi.org/10.2210/pdb4ID7/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2012-12-11 Released: 2013-01-30 
• Deposition Author(s): Jin, M., Wang, J., Kleinberg, A., Kadalbajoo, M., Siu, K., Cooke, A., Bittner, M., Yao, Y., Thelemann, A., Ji, Q., Bhagwat, S., Crew, A.P., Pachter, J., Epstein, D., Mulvihill, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Discovery of potent, selective and orally bioavailable imidazo[1,5-a]pyrazine derived ACK1 inhibitors.

Jin, M., Wang, J., Kleinberg, A., Kadalbajoo, M., Siu, K.W., Cooke, A., Bittner, M.A., Yao, Y., Thelemann, A., Ji, Q., Bhagwat, S., Mulvihill, K.M., Rechka, J.A., Pachter, J.A., Crew, A.P., Epstein, D., Mulvihill, M.J.

(2013) Bioorg Med Chem Lett 23: 979-984

• PubMed: 23317569 
• DOI: https://doi.org/10.1016/j.bmcl.2012.12.042
• Primary Citation of Related Structures:  
  4ID7


• PubMed Abstract: 
  

  This Letter describes the medicinal chemistry effort towards a series of novel imidazo[1,5-a]pyrazine derived inhibitors of ACK1. Virtual screening led to the discovery of the initial hit, and subsequent exploration of structure-activity relationships and optimization of drug metabolism and pharmacokinetic properties led to the identification of potent, selective and orally bioavailable ACK1 inhibitors.

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Organizational Affiliation: 

OSI Pharmaceuticals, LLC, A Wholly-Owned Subsidiary of Astellas US LLC, 1 Bioscience Park Drive, Farmingdale, NY 11735, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 31.69 kDa 
• Atom Count: 2,192 
• Modelled Residue Count: 268 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activated CDC42 kinase 1	A	273	Homo sapiens	Mutation(s): 0  Gene Names: ACK1, TNK2 EC: 2.7.10.2 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q07912 (Homo sapiens) Explore Q07912  Go to UniProtKB:  Q07912
PHAROS:  Q07912 GTEx:  ENSG00000061938

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1G0	B [auth A]	cis-3-[8-amino-1-(4-phenoxyphenyl)imidazo[1,5-a]pyrazin-3-yl]cyclobutanol C22 H20 N4 O2 SAFIVUCEBPHLEO-IYBDPMFKSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
1G0	BindingDB:  4ID7	IC50: 152.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.659	α = 90
b = 94.659	β = 90
c = 187.267	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Jin, M., Wang, J., Kleinberg, A., Kadalbajoo, M., Siu, K., Cooke, A., Bittner, M., Yao, Y., Thelemann, A., Ji, Q., Bhagwat, S., Crew, A.P., Pachter, J., Epstein, D., Mulvihill, M.J.

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2013-02-13
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations