3NW5

Crystal structure of insulin-like growth factor 1 receptor (IGF-1R-WT) complex with a carbon-linked proline isostere inhibitor (11B)

• PDB DOI: https://doi.org/10.2210/pdb3NW5/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2010-07-09 Released: 2010-07-28 
• Deposition Author(s): Sack, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.254 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Proline isosteres in a series of 2,4-disubstituted pyrrolo[1,2-f][1,2,4]triazine inhibitors of IGF-1R kinase and IR kinase.

Sampognaro, A.J., Wittman, M.D., Carboni, J.M., Chang, C., Greer, A.F., Hurlburt, W.W., Sack, J.S., Vyas, D.M.

(2010) Bioorg Med Chem Lett 20: 5027-5030

• PubMed: 20675137 
• DOI: https://doi.org/10.1016/j.bmcl.2010.07.045
• Primary Citation of Related Structures:  
  3NW5, 3NW6, 3NW7


• PubMed Abstract: 
  

  Pyrrolidine, pyrrolidinone, carbocyclic, and acyclic groups were used as isosteric proline replacements in a series of insulin-like growth factor I receptor kinase/insulin receptor kinase inhibitors. Examples that were similar in potency to proline-containing reference compounds were shown to project a key fluoropyridine amide into a common space, while less potent compounds were not able to do so for reasons of stereochemistry or structural rigidity.

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Organizational Affiliation: 

Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, Princeton, NJ 08543-5400, USA. [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: 35.47 kDa 
• Atom Count: 2,645 
• Modelled Residue Count: 302 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-like growth factor 1 receptor	A	307	Homo sapiens	Mutation(s): 0  Gene Names: IGF1R EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08069 (Homo sapiens) Explore P08069  Go to UniProtKB:  P08069
PHAROS:  P08069 GTEx:  ENSG00000140443

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LGX	B [auth A]	N-(5-cyclopropyl-1H-pyrazol-3-yl)-2-{(2R)-1-[(6-fluoropyridin-3-yl)carbonyl]pyrrolidin-2-yl}pyrrolo[2,1-f][1,2,4]triazin-4-amine C22 H21 F N8 O XXGADWBTSMHVDF-MRXNPFEDSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LGX	Binding MOAD:  3NW5	IC50: 8400 (nM) from 1 assay(s)
	PDBBind:  3NW5	IC50: 8400 (nM) from 1 assay(s)
	BindingDB:  3NW5	IC50: 8400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.254 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.642	α = 90
b = 41.289	β = 120.21
c = 78.183	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Sack, J.S.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations