9RIS | pdb_00009ris

Crystal structure of human IDO1 in complex with iDeg-1

• PDB DOI: https://doi.org/10.2210/pdb9RIS/pdb

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


• Deposited: 2025-06-11 Released: 2025-10-01 
• Deposition Author(s): Lucas, B., Lucas, M., Ziegler, S., Waldmann, H., Gasper, R.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Identification of a Monovalent Pseudo-Natural Product Degrader Class Supercharging Degradation of IDO1 by its native E3 KLHDC3

Lucas, B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.19 kDa 
• Atom Count: 3,075 
• Modeled Residue Count: 365 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Indoleamine 2,3-dioxygenase 1	A	404	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
A1JGL (Subject of Investigation/LOI)	D [auth A]	[(1~{R},2~{S},6~{S},8~{R})-4-(4-~{tert}-butylphenyl)sulfonyl-9,9-dimethyl-4-azatricyclo[6.1.1.0^{2,6}]decan-2-yl]methyl ~{N}-(4-methylphenyl)carbamate C30 H40 N2 O4 S WZIVXKXJEWHYHH-RCLWPAGBSA-N
PGE	B [auth A], C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.27	α = 90
b = 110.17	β = 90
c = 36.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Lucas, B., Lucas, M., Ziegler, S., Waldmann, H., Gasper, R.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release