8YTE

Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide

PDB DOI: https://doi.org/10.2210/pdb8YTE/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.249
R-Value Work: 0.197
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.4c00715
Primary Citation of 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.

Organizational Affiliation

Biopharmaceutical Research Division, Shionogi Pharmaceutical Research Center, Toyonaka , Osaka 561-0825, Japan.

Macromolecule Content

Total Structure Weight: 26.39 kDa
Atom Count: 1,864
Modelled Residue Count: 224
Deposited Residue Count: 232
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity nerve growth factor receptor	A, C	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04629
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrocyclic Peptide	B, D	14	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GM1 (Subject of Investigation/LOI) Query on GM1 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain N [auth D] MOL2 format, chain H [auth B] MOL2 format, chain N [auth D] mmCIF format, chain H [auth B] mmCIF format, chain N [auth D]	H [auth B], N [auth D]	AMINOMETHYLAMIDE C₂ H₆ N₂ O BEBCJVAWIBVWNZ-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain N [auth D]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth C] E [auth A], F [auth A], G [auth A], I [auth B], J [auth C], K [auth C], L [auth C], M [auth C], O [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D]