Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 97193.10 
• Atom Count: 6056 
• Residue Count: 846 
• Unique protein chains: 1

4PK5

Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with Amg-1

• DOI: 10.2210/pdb4PK5/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2014-05-13 Released: 2014-09-03 
• Deposition Author(s): Kohno, T., Tojo, S., Ishii, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.256 
• R-Value Work: 0.185 

Literature

Crystal Structures and Structure-Activity Relationships of Imidazothiazole Derivatives as IDO1 Inhibitors.

Tojo, S., Kohno, T., Tanaka, T., Kamioka, S., Ota, Y., Ishii, T., Kamimoto, K., Asano, S., Isobe, Y.

(2014) Acs Med.Chem.Lett. 5: 1119-1123

• PubMed: 25313323 
• DOI: 10.1021/ml500247w
• Primary Citation of Related Structures:  
  4PK6


• PubMed Abstract: 
  

Indoleamine 2,3-dioxygenase 1 (IDO1) is considered as a promising target for the treatment of several diseases, including neurological disorders and cancer. We report here the crystal structures of two IDO1/IDO1 inhibitor complexes, one of which shows that Amg-1 is directly bound to the heme iron of IDO1 with a clear induced fit. We also describe the identification and preliminary optimization of imidazothiazole derivatives as novel IDO1 inhibitors. Using our crystal structure information and structure-activity relationships (SAR) at the pocket-B of IDO1, we found a series of urea derivatives as potent IDO1 inhibitors and revealed that generation of an induced fit and the resulting interaction with Phe226 and Arg231 are essential for potent IDO1 inhibitory activity. The results of this study are very valuable for understanding the mechanism of IDO1 activation, which is very important for structure-based drug design (SBDD) to discover potent IDO1 inhibitors.

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Organizational Affiliation: 

Dainippon Sumitomo Pharma Co., Ltd. , 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-0022, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Indoleamine 2,3-dioxygenase 1	A, B	423	Homo sapiens	Mutation(s): 0  Gene Names: IDO1 (IDO, INDO) EC: 1.13.11.52
Find proteins for P14902 (Homo sapiens) Go to Gene View: IDO1 Go to UniProtKB:  P14902

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PKJ	A, B	N-(1,3-benzodioxol-5-yl)-2-{[5-(4-methylphenyl)[1,3]thiazolo[2,3-c][1,2,4]triazol-3-yl]sulfanyl}acetamide C20 H16 N4 O3 S2 XYXNYQAJSYUYNZ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PKJ	IC50: 3000 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.256 
• R-Value Work: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 84.799	α = 90.00
b = 90.414	β = 90.00
c = 131.757	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-13 
• Released Date: 2014-09-03 
• Deposition Author(s): Kohno, T., Tojo, S., Ishii, T.

Revision History 

• Version 1.0: 2014-09-03
  Type: Initial release
• Version 1.1: 2014-10-29
  Type: Database references