SMTL ID : 8hyi.1

Crystal structure of human P-cadherin MEC12 (X dimer) in complex with 2-(2-methyl-5-phenyl-1H-indole-3-yl)ethan-1-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

2 x 22R: 2-(2-methyl-5-phenyl-1H-indole-3-yl)ethan-1-amine(Non-covalent)

22R.1: 7 residues within 4Å: Chain A: Q.20, R.21, L.22 Chain B: K.74, I.98, T.100, Y.141 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.22, B:I.98 Hydrogen bonds: A:R.21 pi-Stacking: B:Y.141 22R.2: 10 residues within 4Å: Chain A: R.69, K.74, I.98, V.99, T.100, D.101, D.138, Y.141, T.142 Chain B: P.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.98, A:I.98, A:D.101, A:T.142 Hydrogen bonds: A:R.69 pi-Stacking: A:Y.141, A:Y.141

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain B: Y.143, M.197, D.198, D.200 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.200 pi-Cation interactions: B:Y.143 DMS.7: 3 residues within 4Å: Chain A: Y.143, M.197, D.200 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.200

6 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: N.103, H.105, D.135, D.137, N.144, D.196 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.105, A:D.135, A:D.137, A:N.144, A:D.196 CA.5: 7 residues within 4Å: Chain A: E.12, E.70, D.101, Q.102, D.104, H.105, D.137 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.12, A:E.70, A:D.101, A:D.104, A:D.137 CA.6: 3 residues within 4Å: Chain A: D.68, E.71, Y.75 No protein-ligand interaction detected (PLIP) CA.8: 6 residues within 4Å: Chain B: N.103, H.105, D.135, D.137, N.144, D.196 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.105, B:D.135, B:D.137, B:N.144, B:D.196 CA.9: 6 residues within 4Å: Chain B: E.12, E.70, D.101, Q.102, D.104, D.137 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.70, B:E.70, B:D.101, B:Q.102, B:D.104 CA.10: 2 residues within 4Å: Chain B: D.68, Y.75 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Senoo, A. et al., Modulation of a conformational ensemble by a small molecule that inhibits key protein-protein interactions involved in cell adhesion. Protein Sci. (2023)

Release Date

2023-08-30

Peptides

Cadherin-3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cadherin-3

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