MolNFT v1 · #37354 · protein

GRP94 in complex with the novel HSP90 inhibitor radester amine

2FYP · Endoplasmin: “GRP94 in complex with the novel HSP90 inhibitor radester amine”. X-ray diffraction, 1 ligand (RDE), 5 pockets (best druggability 0.63). MolNFT v1 #37354 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2FYP
Type: protein
Length: 464 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endoplasmin
UniProt: P41148
Ligands: RDE
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Endoplasmin	protein	232	39% helix, 23% strand	P41148

Ligands and binding sites

RDE · 2-(3-amino-2,5,6-trimethoxyphenyl)ethyl 5-chloro-2,4-dihydroxybenzoate · ligand · 2 copies · chains A, B
PG4 · Tetraethylene glycol · additive · 8 copies · chains A, B
1PE · Pentaethylene glycol · additive · chains A, 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	264	0.63	0.81	29	RDE
2	242	0.63	0.81	27	RDE
3	359	0.58	0.76	37	1PE
4	86	0.33	0.74	23	PG4
5	62	0.27	0.73	15	PG4

Interfaces

1 interface between chains.

A–B · 458 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

2FYP · GRP94 in complex with the novel HSP90 Inhibitor Radester amine · 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 A against A, TM-score 0.80

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 2FYP · PDBe 2FYP · UniProt P41148

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