8YTD | pdb_00008ytd

Crystal Structure of TrkA D5 domain in complex with two different macrocyclic peptides

• PDB DOI: https://doi.org/10.2210/pdb8YTD/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-25 Released: 2024-07-10 
• Deposition Author(s): Yamada, T., Mihara, K., Ueda, T., Yamauchi, D., Shimizu, M., Ando, A., Mayumi, K., Nakata, Z., Mikamiyama, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Discovery and Hit to Lead Optimization of Macrocyclic Peptides as Novel Tropomyosin Receptor Kinase A Antagonists.

Yamada, T., Mihara, K., Ueda, T., Yamauchi, D., Shimizu, M., Ando, A., Mayumi, K., Nakata, Z., Mikamiyama, H.

(2024) J Med Chem 67: 11197-11208

• PubMed: 38950284 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c00715
• Primary Citation Related Structures: 
  8YTD, 8YTE


• PubMed Abstract: 
  

  Tropomyosin receptor kinases (Trks) are receptor tyrosine kinases activated by neurotrophic factors, called neurotrophins. Among them, TrkA interacts with the nerve growth factor (NGF), which leads to pain induction. mRNA-display screening was carried out to discover a hit compound 2 , which inhibits protein-protein interactions between TrkA and NGF. Subsequent structure optimization improving phosphorylation inhibitory activity and serum stability was pursued using a unique process that took advantage of the peptide being synthesized by translation from mRNA. This gave peptide 19 , which showed an analgesic effect in a rat incisional pain model. The peptides described here can serve as a new class of analgesics, and the structure optimization methods reported provide a strategy for discovering new peptide drugs.

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Organizational Affiliation: 
• Biopharmaceutical Research Division, Shionogi Pharmaceutical Research Center, Toyonaka , Osaka 561-0825, Japan.
Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, Toyonaka , Osaka 561-0825, Japan.
Pharmaceutical Development Division, Yodoyabashi Office, Osaka , Osaka 541-0042, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.38 kDa 
• Atom Count: 1,103 
• Modeled Residue Count: 135 
• Deposited Residue Count: 135 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity nerve growth factor receptor	A	102	Homo sapiens	Mutation(s): 0  Gene Names: NTRK1, MTC, TRK, TRKA EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens) Explore P04629  Go to UniProtKB:  P04629
PHAROS:  P04629 GTEx:  ENSG00000198400

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrocyclic Peptide	B	15	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrocyclic Peptide	C	18	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEA	C	L-PEPTIDE LINKING	C10 H13 N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.374	α = 90
b = 50.374	β = 90
c = 143.959	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Yamada, T., Mihara, K., Ueda, T., Yamauchi, D., Shimizu, M., Ando, A., Mayumi, K., Nakata, Z., Mikamiyama, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release
  
• Version 1.1: 2024-07-17
  Changes: Database references
• Version 1.2: 2024-07-24
  Changes: Database references