5J6D | pdb_00005j6d

Discovery of acyl guanidine tryptophan hydroxylase-1 inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.248 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of acyl guanidine tryptophan hydroxylase-1 inhibitors.

Goldberg, D.R.De Lombaert, S.Aiello, R.Bourassa, P.Barucci, N.Zhang, Q.Paralkar, V.Stein, A.J.Valentine, J.Zavadoski, W.

(2016) Bioorg Med Chem Lett 26: 2855-2860

  • DOI: https://doi.org/10.1016/j.bmcl.2016.04.057
  • Primary Citation Related Structures: 
    5J6D

  • PubMed Abstract: 

    An increasing number of diseases have been linked to a dysfunctional peripheral serotonin system. Given that tryptophan hydroxylase 1 (TPH1) is the rate limiting enzyme in the biosynthesis off serotonin, it represents an attractive target to regulate peripheral serotonin. Following up to our first disclosure, we report a new chemotype of TPH1 inhibitors where-by the more common central planar heterocycle has been replaced with an open-chain, acyl guanidine surrogate. Through our work, we found that compounds of this nature provide highly potent TPH1 inhibitors with favorable physicochemical properties that were effective in reducing murine intestinal 5-HT in vivo. Furthermore, we obtained a high resolution (1.90Å) X-ray structure crystal structure of one of these inhibitors (compound 51) that elucidated the active conformation along with revealing a dimeric form of TPH1 for the first time.


  • Organizational Affiliation
    • Karos Pharmaceuticals, 401 Winchester Ave., 5 Science Park, New Haven, CT 06511, United States. Electronic address: dgoldberg@kineta.us.

Macromolecule Content 

  • Total Structure Weight: 72.54 kDa 
  • Atom Count: 4,335 
  • Modeled Residue Count: 540 
  • Deposited Residue Count: 614 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tryptophan 5-hydroxylase 1
A, B
307Homo sapiensMutation(s): 0 
Gene Names: TPH1TPHTPRHTRPH
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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6H5

Query on 6H5



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
4-[(N-{[2-(3-methoxyphenoxy)-6-(piperidin-1-yl)phenyl]methyl}carbamimidoyl)carbamoyl]-L-phenylalanine
C30 H35 N5 O5
UDMPHIGEFLMAIW-VWLOTQADSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.248 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.726α = 90
b = 63.561β = 90
c = 156.468γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-15
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description