Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.11 kDa 
• Atom Count: 1798 
• Residue Count: 208 
• Unique protein chains: 1

1FBZ

Structure-based design of a novel, osteoclast-selective, nonpeptide Src SH2 inhibitor with in vivo anti-resorptive activity

• DOI: 10.2210/pdb1FBZ/pdb

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


• Deposited: 2000-07-17 Released: 2000-08-23 
• Deposition Author(s): Shakespeare, W., Yang, M., Bohacek, R., Cerasoli, F., Stebbis, K., Sundaramoorthi, R., Vu, C., Pradeepan, S., Metcalf, C., Haraldson, C., Merry, T., Dalgarno, D., Narula, S., Hatada, M., Lu, X., Van Schravendijk, M.R., Adams, S., Violette, S., Smith, J., Guan, W., Bartlett, C., Herson, J., Iuliucci, J., Weigele, M., Sawyer, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.360 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 

Literature

Structure-based design of an osteoclast-selective, nonpeptide src homology 2 inhibitor with in vivo antiresorptive activity.

Shakespeare, W., Yang, M., Bohacek, R., Cerasoli, F., Stebbins, K., Sundaramoorthi, R., Azimioara, M., Vu, C., Pradeepan, S., Metcalf, C., Haraldson, C., Merry, T., Dalgarno, D., Narula, S., Hatada, M., Lu, X., van Schravendijk, M.R., Adams, S., Violette, S., Smith, J., Guan, W., Bartlett, C., Herson, J., Iuliucci, J., Weigele, M., Sawyer, T.

(2000) Proc Natl Acad Sci U S A 97: 9373-9378

• PubMed: 10944210 
• DOI: 10.1073/pnas.97.17.9373
• Primary Citation of Related Structures:  
  1FBZ


• PubMed Abstract: 
  

Targeted disruption of the pp60(src) (Src) gene has implicated this tyrosine kinase in osteoclast-mediated bone resorption and as a therapeutic target for the treatment of osteoporosis and other bone-related diseases. Herein we describe the discovery of a nonpeptide inhibitor (AP22408) of Src that demonstrates in vivo antiresorptive activity. Based on a cocrystal structure of the noncatalytic Src homology 2 (SH2) domain of Src complexed with citrate [in the phosphotyrosine (pTyr) binding pocket], we designed 3',4'-diphosphonophenylalanine (Dpp) as a pTyr mimic. In addition to its design to bind Src SH2, the Dpp moiety exhibits bone-targeting properties that confer osteoclast selectivity, hence minimizing possible undesired effects on other cells that have Src-dependent activities. The chemical structure AP22408 also illustrates a bicyclic template to replace the post-pTyr sequence of cognate Src SH2 phosphopeptides such as Ac-pTyr-Glu-Glu-Ile (1). An x-ray structure of AP22408 complexed with Lck (S164C) SH2 confirmed molecular interactions of both the Dpp and bicyclic template of AP22408 as predicted from molecular modeling. Relative to the cognate phosphopeptide, AP22408 exhibits significantly increased Src SH2 binding affinity (IC(50) = 0.30 microM for AP22408 and 5.5 microM for 1). Furthermore, AP22408 inhibits rabbit osteoclast-mediated resorption of dentine in a cellular assay, exhibits bone-targeting properties based on a hydroxyapatite adsorption assay, and demonstrates in vivo antiresorptive activity in a parathyroid hormone-induced rat model.

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Organizational Affiliation: 

ARIAD Pharmaceuticals, Inc., Cambridge, MA 02139, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE LCK	A, B	104	Homo sapiens	Mutation(s): 0  Gene Names: LCK EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
Find proteins for P06239 (Homo sapiens) Explore P06239  Go to UniProtKB:  P06239
NIH Common Fund Data Resources
PHAROS:  P06239 GTEx:  ENSG00000182866

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CC1	A, B	{4-[2-ACETYLAMINO-2-(3-CARBAMOYL-2-CYCLOHEXYLMETHOXY-6,7,8,9-TETRAHYDRO-5H-BENZOCYCLOHEPTEN-5YLCARBAMOYL)-ETHYL]-2-PHOSPHONO-PHENYL}-PHOSPHONIC ACID C30 H41 N3 O10 P2 SPSGYTWOIGAABK-DQEYMECFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.360 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.87	α = 90
b = 56.26	β = 90
c = 102.77	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-07-17 
• Released Date: 2000-08-23 
Deposition Author(s): Shakespeare, W., Yang, M., Bohacek, R., Cerasoli, F., Stebbis, K., Sundaramoorthi, R., Vu, C., Pradeepan, S., Metcalf, C., Haraldson, C., Merry, T., Dalgarno, D., Narula, S., Hatada, M., Lu, X., Van Schravendijk, M.R., Adams, S., Violette, S., Smith, J., Guan, W., Bartlett, C., Herson, J., Iuliucci, J., Weigele, M., Sawyer, T.

Revision History 

• Version 1.0: 2000-08-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance