3HFB

Crystal structure of human tryoptophan hydroxylase type 1 with LP-534193


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Mechanism of Inhibition of Novel Tryptophan Hydroxylase Inhibitors Revealed by Co-crystal Structures and Kinetic Analysis.

Cianchetta, G.Stouch, T.Yu, W.Shi, Z.C.Tari, L.W.Swanson, R.V.Hunter, M.J.Hoffman, I.D.Liu, Q.

(2010) Curr Chem Genomics 4: 19-26

  • DOI: https://doi.org/10.2174/1875397301004010019
  • Primary Citation of Related Structures:  
    3HF8, 3HFB

  • PubMed Abstract: 

    Trytophan Hydroxylase Type I (TPH1), most abundantly expressed in the gastrointestinal tract, initiates the synthesis of serotonin by catalyzing hydroxylation of tryptophan in the presence of biopterin and oxygen. We have previously described three series of novel, periphery-specific TPH1 inhibitors that selectively deplete serotonin in the gastrointestinal tract. We have now determined co-crystal structures of TPH1 with three of these inhibitors at high resolution. Analysis of the structural data showed that each of the three inhibitors fills the tryptophan binding pocket of TPH1 without reaching into the binding site of the cofactor pterin, and induces major conformational changes of the enzyme. The enzyme-inhibitor complexes assume a compact conformation that is similar to the one in tryptophan complex. Kinetic analysis showed that all three inhibitors are competitive versus the substrate tryptophan, consistent with the structural data that the compounds occupy the tryptophan binding site. On the other hand, all three inhibitors appear to be uncompetitive versus the cofactor 6-methyltetrahydropterin, which is not only consistent with the structural data but also indicate that the hydroxylation reaction follows an ordered binding mechanism in which a productive complex is formed only if tryptophan binds only after pterin, similar to the kinetic mechanisms of tyrosine and phenylalanine hydroxylase.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Lexicon Pharmaceuticals, Inc., 350 Carter Rd., Princeton, New Jersey, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan 5-hydroxylase 1290Homo sapiensMutation(s): 2 
EC: 1.14.16.4
UniProt & NIH Common Fund Data Resources
Find proteins for P17752 (Homo sapiens)
Explore P17752 
Go to UniProtKB:  P17752
PHAROS:  P17752
GTEx:  ENSG00000129167 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17752
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ML4
Query on ML4

Download Ideal Coordinates CCD File 
C [auth A]4-(5-{[(2'-methylbiphenyl-2-yl)methyl]amino}pyrazin-2-yl)-L-phenylalanine
C27 H26 N4 O2
LQRILFQFPLOLRC-DEOSSOPVSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ML4 PDBBind:  3HFB Ki: 30 (nM) from 1 assay(s)
BindingDB:  3HFB IC50: 40 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.354α = 90
b = 58.143β = 96.77
c = 56.625γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-21
    Changes: Data collection