Research workbench
Structure of GRP94 bound to methyl 2-[2-(2-benzylpyridin-3-YL)ETHYL]- 3-chloro-4,6-dihydroxybenzoate, a pan-HSP90 inhibitor
Analyse Structure of GRP94 bound to methyl 2-[2-(2-benzylpyridin-3-YL)ETHYL]… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ASQ
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmin
- UniProt
- P41148
- Ligands
- VC4
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmin | protein | 217 | 39% helix, 25% strand | P41148 |
| B | Endoplasmin | protein | 218 | 39% helix, 25% strand | P41148 |
Ligands and binding sites
- VC4 · methyl 2-[2-(2-benzylpyridin-3-yl)ethyl]-3-chloro-4,6-dihydroxybenzoate · ligand · 2 copies · chains A, B
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · 13 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.63 | 0.80 | 29 | VC4 |
| 2 | 299 | 0.63 | 0.80 | 28 | VC4 |
| 3 | 400 | 0.58 | 0.75 | 45 | PEG, PE8 |
| 4 | 96 | 0.34 | 0.74 | 22 | PE8 |
| 5 | 70 | 0.31 | 0.74 | 23 | PE8 |
Interfaces
1 interface between chains.
- A–B · 170 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6ASQ · Structure of Grp94 bound to methyl 2-[2-(2-benzylpyridin-3-yl)ethyl]-3-chloro-4,6-dihydrox… · 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 0.86
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 6ASQ · PDBe 6ASQ · UniProt P41148
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