5L01 | pdb_00005l01

Tryptophan 5-hydroxylase in complex with inhibitor (3~{S})-8-[2-azanyl-6-[(1~{R})-1-(4-chloranyl-2-phenyl-phenyl)-2,2,2-tris(fluoranyl)ethoxy]pyrimidin-4-yl]-2,8-diazaspiro[4.5]decane-3-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.214 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5L01

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Optimization of spirocyclic proline tryptophan hydroxylase-1 inhibitors.

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

(2017) Bioorg Med Chem Lett 27: 413-419

  • DOI: https://doi.org/10.1016/j.bmcl.2016.12.053
  • Primary Citation Related Structures: 
    5L01, 5TPG

  • PubMed Abstract: 

    As a follow-up to the discovery of our spirocyclic proline-based TPH1 inhibitor lead, we describe the optimization of this scaffold. Through a combination of X-ray co-crystal structure guided design and an in vivo screen, new substitutions in the lipophilic region of the inhibitors were identified. This effort led to new TPH1 inhibitors with in vivo efficacy when dosed as their corresponding ethyl ester prodrugs. In particular, 15b (KAR5585), the prodrug of the potent TPH1 inhibitor 15a (KAR5417), showed robust reduction of intestinal serotonin (5-HT) levels in mice. Furthermore, oral administration of 15b generated high and sustained systemic exposure of the active parent 15a in rats and dogs. KAR5585 was selected for further pharmacological evaluation in disease models associated with a dysfunctional peripheral 5-HT system.


  • 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: 51.68 kDa 
  • Atom Count: 2,461 
  • Modeled Residue Count: 283 
  • Deposited Residue Count: 444 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tryptophan 5-hydroxylase 1444Homo 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
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6Z4

Query on 6Z4



Download:Ideal Coordinates CCD File
C [auth A](3~{S})-8-[2-azanyl-6-[(1~{R})-1-(4-chloranyl-2-phenyl-phenyl)-2,2,2-tris(fluoranyl)ethoxy]pyrimidin-4-yl]-2,8-diazaspiro[4.5]decane-3-carboxylic acid
C27 H27 Cl F3 N5 O3
ZNSPHKJFQDEABI-NZQKXSOJSA-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
6Z4 BindingDB:  5L01 IC50: 33 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.214 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.302α = 90
b = 58.167β = 97.49
c = 56.678γ = 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: 2017-01-25
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description