8QV7

Crystal structure of human TDO with alpha-methyl-L-tryptophan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Discovery and binding mode of small molecule inhibitors of the apo form of human TDO2.

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

(2024) Sci Rep 14: 27937-27937

  • DOI: https://doi.org/10.1038/s41598-024-78981-4
  • Primary Citation of Related Structures:  
    8QV7, 8R5Q, 8R5R, 9EZJ

  • PubMed Abstract: 

    Tryptophan-2,3-dioxygenase (TDO2) and indoleamine-2,3-dioxygenase (IDO1) are structurally distinct heme enzymes that catalyze the conversion of L-tryptophan to N-formyl-kynurenine, and play important roles in metabolism, inflammation, and tumor immune surveillance. The enzymes can adopt an inactive, heme-free (apo) state or an active, heme-containing (holo) state, with the balance between them varying dynamically according to biological conditions. Inhibitors of holo-TDO2 are known but, despite several advantages of the heme-free state as a drug target, no inhibitors of apo-TDO2 have been reported. We describe the discovery of the first apo-TDO2 binding inhibitors, to our knowledge, and their inhibition of cellular TDO2 activity at low nanomolar concentrations. The crystal structure of a potent, small molecule inhibitor bound to apo-TDO2 reveals its detailed binding interactions within the large, hydrophobic heme binding pocket of the active site.


  • Organizational Affiliation

    Drug discovery, Idorsia Pharmaceuticals Limited, Hegenheimermattweg 91, Allschwil, Basel-Land, 4123, Switzerland. carina.lotz@idorsia.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan 2,3-dioxygenase
A, B, C, D
355Homo sapiensMutation(s): 0 
Gene Names: TDO2
EC: 1.13.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P48775 (Homo sapiens)
Explore P48775 
Go to UniProtKB:  P48775
PHAROS:  P48775
GTEx:  ENSG00000151790 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48775
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.285α = 90
b = 90.756β = 120.75
c = 132.774γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
  • Version 2.0: 2024-12-04
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary