6X5Y

IDO1 in complex with compound 4

• PDB DOI: https://doi.org/10.2210/pdb6X5Y/pdb

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


• Deposited: 2020-05-27 Released: 2021-06-02 
• Deposition Author(s): Lesburg, C.A., Lammens, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.272 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 

Starting Model: experimental

Literature

Utilization of MetID and Structural Data to Guide Placement of Spiro and Fused Cyclopropyl Groups for the Synthesis of Low Dose IDO1 Inhibitors

Hopkins, B., Zhang, H., Bharathan, I., Li, D., Pu, Q., Zhou, H., Martinot, T., Fradera, X., Lammens, A., Lesburg, C.A., Ballard, J., Knemeyer, I., Otte, K., Solban, N., Vincent, S., Miller, J.R., Cheng, M., Geda, P., Smotrov, N., Song, X., Spacciapoli, P., Bennett, D.J., Han, Y.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.52 kDa 
• Atom Count: 6,023 
• Modelled Residue Count: 746 
• 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) Go to UniProtKB:  P14902
PHAROS:  P14902 GTEx:  ENSG00000131203

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URJ (Subject of Investigation/LOI)	C [auth A], D [auth B]	4-fluoro-N-{1-[5-(2-methylpyrimidin-4-yl)-5,6,7,8-tetrahydro-1,5-naphthyridin-2-yl]cyclopropyl}benzamide C23 H22 F N5 O KKAMMYSFTPLTDH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
URJ	BindingDB:  6X5Y	IC50: min: 1.2, max: 64 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.272 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.94	α = 90
b = 92.157	β = 90
c = 130.126	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-02 
Deposition Author(s): Lesburg, C.A., Lammens, A.

Revision History  

• Version 1.0: 2021-06-02
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary