3HF8

Crystal structure of human tryoptophan hydroxylase type 1 with bound LP-533401 and Fe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.2174/1875397301004010019
  • Primary Citation of Related Structures:  
    3HFB, 3HF8

  • 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 s ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan 5-hydroxylase 1A290Homo sapiensMutation(s): 0 
Gene Names: TPH1TPHTPRHTRPH
EC: 1.14.16.4
Find proteins for P17752 (Homo sapiens)
Explore P17752 
Go to UniProtKB:  P17752
NIH Common Fund Data Resources
PHAROS  P17752
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ML0
Query on ML0

Download CCD File 
A
4-{2-amino-6-[(1R)-2,2,2-trifluoro-1-(3'-fluorobiphenyl-4-yl)ethoxy]pyrimidin-4-yl}-L-phenylalanine
C27 H22 F4 N4 O3
JZWUKILTKYJLCN-XUZZJYLKSA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ML0Ki :  310   nM  PDBBind
ML0Ki:  310   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.278α = 90
b = 58.238β = 97.15
c = 56.554γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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