SMTL ID : 8yte.2 (1 other biounit)

Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: Q.89, A.90, S.91 No protein-ligand interaction detected (PLIP) EDO.2: 4 residues within 4Å: Chain A: H.11, P.22, F.23, G.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.64 Water bridges: A:H.63 EDO.3: 5 residues within 4Å: Chain A: S.32, L.33, L.82, A.84 Ligands: GM1.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.33 EDO.4: 1 residues within 4Å: Chain A: N.38 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain B: F.2, Y.5, P.6, G.8, V.13, C.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.5, B:C.14

1 x GM1: AMINOMETHYLAMIDE(Covalent)

GM1.5: 5 residues within 4Å: Chain A: L.33, R.34 Chain B: V.13, C.14 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.33, A:R.34

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

High affinity nerve growth factor receptor

Macrocyclic Peptide

Related Entries With Identical Sequence