MolNFT v1 · #175301 · protein

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)

7CME · Cadherin-3: “Crystal structure of human P-cadherin MEC12 (X dimer) in complex with…”. X-ray diffraction, 2 ligands (G60, CA), 3 pockets (best druggability 0.61). MolNFT v1 #175301 on GenesisL1: 3D structure, binding sites and…

PDB: 7CME
Type: protein
Length: 428 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cadherin-3
UniProt: P22223
Ligands: G60, CA
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cadherin-3	protein	214	3% helix, 46% strand	P22223

Ligands and binding sites

G60 · 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine · ligand · 3 copies · chains A, B
CA · Calcium ion · metal · 6 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	281	0.61	0.79	34	G60
2	251	0.59	0.79	30	G60
3	62	0.37	0.79	14	DMS

Interfaces

1 interface between chains.

A–B · 1730 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

7CME · Crystal structure of human P-cadherin MEC12 (X dimer) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
P22223 · AlphaFold monomer V2.0 prediction for cadherin-3 (P22223) · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P22223
Elsewhere: RCSB PDB 7CME · PDBe 7CME · UniProt P22223

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