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Structure of molecular chaperone GRP94 bound to selective inhibitor methyl 2-[2-(2-BENZYLPHENYL)ETHYL]-3-chloro-4,6-dihydroxybenzoate

Analyse Structure of molecular chaperone GRP94 bound to selective inhibitor methyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AOM
Type: protein
Length: 427 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endoplasmin
UniProt: P41148
Ligands: VC5
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endoplasmin	protein	214	38% helix, 25% strand	P41148
B	Endoplasmin	protein	213	37% helix, 25% strand	P41148

Ligands and binding sites

VC5 · methyl 2-[2-(2-benzylphenyl)ethyl]-3-chloro-4,6-dihydroxybenzoate · ligand · 2 copies · chains A, B
P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 15 copies · chains A, B
GOL · Glycerol · additive · chains A
PEG · Di(hydroxyethyl)ether · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	279	0.65	0.81	28	VC5
2	230	0.62	0.81	23	VC5
3	403	0.59	0.75	46	P33
4	94	0.32	0.73	22	P33
5	70	0.29	0.73	20	P33

Interfaces

1 interface between chains.

A–B · 203 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6AOM · Structure of molecular chaperone Grp94 bound to selective inhibitor methyl… · the same entry in another collection · chain A against A, TM-score 1.00
P41148 · AlphaFold monomer V2.0 prediction for endoplasmin (P41148) · a predicted model of the same protein · chain B against A, TM-score 0.87

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 P41148
Elsewhere: RCSB PDB 6AOM · PDBe 6AOM · UniProt P41148

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