3LVP

Crystal structure of bisphosphorylated IGF1-R Kinase domain (2P) in complex with a bis-azaindole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3LVP/pdb

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


• Deposited: 2010-02-22 Released: 2010-07-21 
• Deposition Author(s): Maignan, S., Marquette, J.P., Guilloteau, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.279 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

Design of Potent IGF1-R Inhibitors Related to Bis-azaindoles

Nemecek, C., Metz, W.A., Wentzler, S., Ding, F.X., Venot, C., Souaille, C., Dagallier, A., Maignan, S., Guilloteau, J.P., Bernard, F., Henry, A., Grapinet, S., Lesuisse, D.

(2010) Chem Biol Drug Des 76: 100-106

• PubMed: 20545947 
• DOI: https://doi.org/10.1111/j.1747-0285.2010.00991.x
• Primary Citation of Related Structures:  
  3LVP


• PubMed Abstract: 
  

  From an azaindole lead, identified in high throughput screen, a series of potent bis-azaindole inhibitors of IGF1-R have been synthesized using rational drug design and SAR based on a in silico binding mode hypothesis. Although the resulting compounds produced the expected improved potency, the model was not validated by the co-crystallization experiments with IGF1-R.

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Organizational Affiliation: 

Medicinal Chemistry, Sanofi-Aventis, 13 Quai Jules Guesde, 94300 Vitry-sur-Seine, France.

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: 155.68 kDa 
• Atom Count: 9,405 
• Modelled Residue Count: 1,159 
• Deposited Residue Count: 1,344 
• 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	336	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PDR	E [auth A], H [auth B], J [auth C], K [auth D]	3-(4-chloro-1H-pyrrolo[2,3-b]pyridin-2-yl)-5,6-dimethoxy-1-methyl-1H-pyrrolo[3,2-b]pyridine C17 H15 Cl N4 O2 ISLVGFDZMORPFI-UHFFFAOYSA-N
EPE	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4	G [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.279 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.220 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.95	α = 90
b = 94.95	β = 90
c = 322.29	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Maignan, S., Marquette, J.P., Guilloteau, J.P.

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description