SMTL ID : 8ytd.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: H.11, T.12, V.14 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.12, A:T.12 EDO.2: 4 residues within 4Å: Chain A: T.12, A.13, A.96, A.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.97 Water bridges: A:A.13 EDO.3: 5 residues within 4Å: Chain A: H.17, H.18, R.67, N.69, Q.70 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.17, A:R.67, A:Q.70 Water bridges: A:H.17, A:H.18 EDO.4: 4 residues within 4Å: Chain A: E.44 Chain B: G.1, F.2, F.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.44, A:E.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamada, T. et al., Discovery and Hit to Lead Optimization of Macrocyclic Peptides as Novel Tropomyosin Receptor Kinase A Antagonists. J.Med.Chem. (2024)

Release Date

2024-07-10

Peptides

High affinity nerve growth factor receptor: A
Macrocyclic Peptide: B
Macrocyclic Peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

High affinity nerve growth factor receptor

Macrocyclic Peptide

Macrocyclic Peptide

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