8PYJ | pdb_00008pyj

Human IGF1R with inhibitor 8

• PDB DOI: https://doi.org/10.2210/pdb8PYJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-07-25 Released: 2023-09-20 
• Deposition Author(s): Dreyer, M.K., Wang, J., Elkins, J.M.
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.302 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Human IGF1R with inhibitor 8

Dreyer, M.K., Wang, J., Elkins, J.M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.43 kDa 
• Atom Count: 2,290 
• Modeled Residue Count: 277 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-like growth factor 1 receptor beta chain	A [auth AAA]	321	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IEA (Subject of Investigation/LOI)	B [auth AAA]	5,5-dimethyl-1-(quinolin-4-ylmethyl)-3-[4-(trifluoromethylsulfonyl)phenyl]imidazolidine-2,4-dione C22 H18 F3 N3 O4 S WXNMKLZXAKKCON-UHFFFAOYSA-N
CD	D [auth AAA]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
ZN	E [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	C [auth AAA]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IEA	BindingDB:  8PYJ	IC50: 460 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.302 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.199 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.3	α = 90
b = 69.3	β = 90
c = 142.804	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Dreyer, M.K., Wang, J., Elkins, J.M.

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	K4DD

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release