8R5Q

Structure of apo TDO with a bound inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8R5Q/pdb

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


• Deposited: 2023-11-17 Released: 2024-01-17 
• Deposition Author(s): Wicki, M., Mac Sweeney, A.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.267 
• R-Value Work: 0.254 
• R-Value Observed: 0.255 

Literature

Discovery and binding mode of a small molecule inhibitor of the apo form of human TDO2

Lotz-Jenne, C., Lange, R., Cren, S., Bourquin, G., Goglia, L., Kimmerlin, T., Wicki, M., Mueller, M., Artico, N., Ackerknecht, S., Joesch, C., Mac Sweeney, A.

(2024) Biorxiv 

• DOI: https://doi.org/10.1101/2024.01.09.574827

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 173.76 kDa 
• Atom Count: 9,960 
• Modelled Residue Count: 1,263 
• Deposited Residue Count: 1,432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan 2,3-dioxygenase	A, B, C, D	358	Homo sapiens	Mutation(s): 0  Gene Names: TDO2
UniProt & NIH Common Fund Data Resources
Find proteins for P48775 (Homo sapiens) Explore P48775  Go to UniProtKB:  P48775
PHAROS:  P48775 GTEx:  ENSG00000151790

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y5N (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], K [auth D]	3-chloranyl-~{N}-[(1~{S})-1-(6-chloranylpyridin-3-yl)-2-phenyl-ethyl]aniline C19 H16 Cl2 N2 FPQMXEJXTNDYME-SFHVURJKSA-N
ZIQ	F [auth A], H [auth B], J [auth C], L [auth D]	alpha-methyl-L-tryptophan C12 H14 N2 O2 ZTTWHZHBPDYSQB-LBPRGKRZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.267 
• R-Value Work: 0.254 
• R-Value Observed: 0.255 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.33	α = 90
b = 132.49	β = 90
c = 135.57	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Wicki, M., Mac Sweeney, A.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release