Crystal structure of human tryptophan hydroxylase 1 in complex with inhibitor KM-06-057

Experimental Data Snapshot

  • Resolution: 1.66 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

Starting Model: experimental
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Structure-Based Design of Xanthine-Imidazopyridines and -Imidazothiazoles as Highly Potent and In Vivo Efficacious Tryptophan Hydroxylase Inhibitors.

Specker, E.Wesolowski, R.Schutz, A.Matthes, S.Mallow, K.Wasinska-Kalwa, M.Winkler, L.Oder, A.Alenina, N.Pleimes, D.von Kries, J.P.Heinemann, U.Bader, M.Nazare, M.

(2023) J Med Chem 66: 14866-14896

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01454
  • Primary Citation of Related Structures:  
    8CJI, 8CJJ, 8CJK, 8CJL, 8CJM, 8CJN, 8CJO

  • PubMed Abstract: 

    Tryptophan hydroxylases catalyze the first and rate-limiting step in the biosynthesis of serotonin, a well-known neurotransmitter that plays an important role in multiple physiological functions. A reduction of serotonin levels, especially in the brain, can cause dysregulation leading to depression or insomnia. In contrast, overproduction of peripheral serotonin is associated with symptoms like carcinoid syndrome and pulmonary arterial hypertension. Recently, we developed a class of TPH inhibitors based on xanthine-benzimidazoles, characterized by a tripartite-binding mode spanning the binding sites of the cosubstrate pterin and the substrate tryptophan and by chelation of the catalytic iron ion. Herein, we describe the structure-based development of a second generation of xanthine-imidiazopyridines and -imidazothiazoles designed to inhibit TPH1 in the periphery while preventing the interaction with TPH2 in the brain. Lead compound 32 (TPT-004) shows superior pharmacokinetic and pharmacodynamic properties as well as efficacy in preclinical models of peripheral serotonin attenuation and colorectal tumor growth.

  • Organizational Affiliation

    Chemical Biology Platform, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan 5-hydroxylase 1326Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P17752 (Homo sapiens)
Explore P17752 
Go to UniProtKB:  P17752
GTEx:  ENSG00000129167 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17752
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UVF (Subject of Investigation/LOI)
Query on UVF

Download Ideal Coordinates CCD File 
C [auth A]3-ethyl-7-(phenylmethyl)-8-(5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-2-ylmethyl)purine-2,6-dione
C22 H24 N6 O2
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Experimental Data & Validation

Experimental Data

  • Resolution: 1.66 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.004α = 90
b = 58.042β = 97.928
c = 59.412γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Helmholtz AssociationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release