3LW0 | pdb_00003lw0

IGF-1RK in complex with ligand MSC1609119A-1

• PDB DOI: https://doi.org/10.2210/pdb3LW0/pdb

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


• Deposited: 2010-02-23 Released: 2010-09-29 
• Deposition Author(s): Graedler, U., Heinrich, T., Boettcher, H., Blaukat, A., Shutes, A., Askew, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.185 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

Allosteric IGF-1R Inhibitors.

Heinrich, T., Gradler, U., Bottcher, H., Blaukat, A., Shutes, A.

(2010) ACS Med Chem Lett 1: 199-203

• PubMed: 24900194 
• DOI: https://doi.org/10.1021/ml100044h
• Primary Citation of Related Structures:  
  3LW0


• PubMed Abstract: 
  

  Targeting allosteric protein sites is a promising approach to interfere selectively with cellular signaling cascades. We have discovered a novel class of allosteric insulin-like growth factor-I receptor (IGF-1R) inhibitors. 3-Cyano-1H-indole-7-carboxylic acid {1-[4-(5-cyano-1H-indol-3-yl)butyl]piperidin-4-yl}amide (10) was found with nanomolar biochemical, micromolar, cellular IGF-1R activity and no relevant interference with cellular insulin receptor signaling up to 30 μM. The allosteric binding site was characterized by X-ray crystallographic studies, and the structural information was used to explain the unique mode of action of this new class of inhibitors.

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Organizational Affiliation: 

Merck Serono, Frankfurter Strasse 250, 64293 Darmstadt, Germany.

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)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 142.33 kDa 
• Atom Count: 10,929 
• Modelled Residue Count: 1,168 
• Deposited Residue Count: 1,216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-like growth factor 1 receptor	A, B, C, D	304	Homo sapiens	Mutation(s): 2  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CCX	E [auth A], F [auth A], G [auth B], H [auth B], J [auth C], K [auth C], M [auth D], N [auth D]	3-cyano-N-{1-[4-(5-cyano-1H-indol-3-yl)butyl]piperidin-4-yl}-1H-indole-7-carboxamide C28 H28 N6 O GVZDPXYOJHKYRC-UHFFFAOYSA-N
GOL	I [auth B], L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.185 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.170 (DCC) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.346	α = 90
b = 189.346	β = 90
c = 115.92	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-29 
Deposition Author(s): Graedler, U., Heinrich, T., Boettcher, H., Blaukat, A., Shutes, A., Askew, B.

Revision History  

• Version 1.0: 2010-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-12-25
  Changes: Advisory, Database references
• Version 1.3: 2023-11-01
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description