SMTL ID : 7cme.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 4 residues within 4Å: Chain A: Y.143, M.197, D.198, D.200 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.200 pi-Cation interactions: A:Y.143 DMS.8: 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

3 x G60: 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine(Non-covalent)

G60.2: 9 residues within 4Å: Chain A: R.69, I.98, V.99, T.100, D.101, D.138, Y.141, T.142 Chain B: P.11 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.98, A:T.100, A:D.101, B:P.11 Hydrogen bonds: A:V.99 Water bridges: B:Q.102 G60.3: 6 residues within 4Å: Chain A: K.106, G.201, S.202, T.203 Chain B: S.202, T.203 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.203, A:G.201 G60.4: 7 residues within 4Å: Chain A: P.11, Q.20, L.22 Chain B: I.98, T.100, Y.141, T.142 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.98, A:P.11 pi-Stacking: B:Y.141, B:Y.141 Hydrogen bonds: A:Q.20

6 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.6: 6 residues within 4Å: Chain A: E.12, E.70, D.101, Q.102, D.104, D.137 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.12, A:E.70, A:Q.102, A:D.104, A:D.137 CA.7: 3 residues within 4Å: Chain A: D.68, E.71, Y.75 No protein-ligand interaction detected (PLIP) CA.9: 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.10: 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.12, B:E.70, B:D.101, B:Q.102, B:D.104 CA.11: 3 residues within 4Å: Chain B: D.68, E.71, Y.75 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Senoo, A. et al., Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion. Commun Biol (2021)

Release Date

2021-09-15

Peptides

Cadherin-3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cadherin-3

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