9WPB | pdb_00009wpb

Crystal structure of human transthyretin (TTR) with pryazole-based stabilizer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.180 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Pyrazole-Based Transthyretin Kinetic Stabilizers Identified Using a Covalent Fluorescent Probe Assay for Selectivity Profiling in Human Serum.

Kim, K.A.Lee, C.Lim, N.Kim, K.W.Lee, Y.H.Choe, J.Kim, S.J.Jeong, J.W.Jeon, E.H.Son, D.H.Park, S.J.Kang, N.S.Shin, H.C.Koo, T.S.Choi, S.

(2025) J Med Chem 68: 26448-26465

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02576
  • Primary Citation Related Structures: 
    9WPB

  • PubMed Abstract: 

    Transthyretin (TTR) amyloidosis arises from the extracellular aggregation of misfolded TTR monomers into β-sheet-rich fibrils, leading to progressive tissue damage. To inhibit this process, we designed and synthesized pyrazole-based kinetic stabilizers targeting the thyroxine-binding sites of TTR. Structure-activity relationship studies revealed that derivatives with hydrophobic trans-alkene linkers and 3,5-substituted pyrazole rings showed enhanced stabilizing potency, particularly those bearing carboxylic acid, amide, or sulfonamide groups. A covalent fluorescent probe derived from trans-styrylpyrazole was developed to selectively react with Lys15, enabling fluorescence probe exclusion and native PAGE assays to evaluate stabilizer selectivity in human serum. Among these, 3,5-dichloropyrazole derivatives exhibited efficacy comparable to that of tafamidis and acoramidis. X-ray crystallography of the TTR- 17 complex confirmed hydrogen bonding with Ser117/117' and electrostatic interactions with Lys15. Pharmacokinetic studies of compounds 16 and 17 demonstrated favorable exposure, bioavailability, and metabolic stability, supporting their preclinical development for hereditary- and wild-type TTR amyloidosis.


  • Organizational Affiliation
    • Department of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 113.97 kDa 
  • Atom Count: 8,082 
  • Modeled Residue Count: 928 
  • Deposited Residue Count: 1,040 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transthyretin
A, B, C, D, E
A, B, C, D, E, F, G, H
130Homo sapiensMutation(s): 0 
Gene Names: TTRPALB
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
PHAROS:  P02766
GTEx:  ENSG00000118271 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02766
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.180 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.948α = 90.03
b = 65.187β = 89.98
c = 84.665γ = 89.99
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentKorea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-06
    Type: Initial release