8U5I | pdb_00008u5i

Crystal Structure of human IDO1 bound to Compound 23

• PDB DOI: https://doi.org/10.2210/pdb8U5I/pdb

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


• Deposited: 2023-09-12 Released: 2024-11-27 
• Deposition Author(s): Steinbacher, S., Lammens, A., Harris, S.F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.219 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Exploiting Stereo-Complexity to Identify Spirocyclic Imidazoisoindoles as Potent and Orally Bioavailable Dual Inhibitors of Indoleamine-2,3-Dioxygenase and Tryptophan-2,3-Dioxygenase

Pastor, R., Harris, S.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 90.75 kDa 
• Atom Count: 6,743 
• Modeled Residue Count: 751 
• Deposited Residue Count: 788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Indoleamine 2,3-dioxygenase 1	A, B	394	Homo sapiens	Mutation(s): 0  Gene Names: IDO1, IDO, INDO EC: 1.13.11.52
UniProt & NIH Common Fund Data Resources
Find proteins for P14902 (Homo sapiens) Explore P14902  Go to UniProtKB:  P14902
PHAROS:  P14902 GTEx:  ENSG00000131203

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
W2Z (Subject of Investigation/LOI)	D [auth A], F [auth B]	(1R,2S)-8-(ethanesulfonyl)-2-[(4R,5S,9aM)-5H-imidazo[5,1-a]isoindol-5-yl]-8-azaspiro[4.5]decan-1-ol C21 H27 N3 O3 S WFTNBEBSRJTXNN-DFQSSKMNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.219 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.862	α = 90
b = 89.888	β = 90
c = 133.52	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Steinbacher, S., Lammens, A., Harris, S.F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release