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HSP90B N-terminal domain with inhibitors

Analyse HSP90B N-terminal domain with inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5UC4
Type: protein
Length: 855 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock protein HSP 90-beta
UniProt: P08238
Ligands: 83S
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heat shock protein HSP 90-beta	protein	219	43% helix, 23% strand	P08238
B, D	Heat shock protein HSP 90-beta	protein	209	44% helix, 23% strand	P08238
C	Heat shock protein HSP 90-beta	protein	218	43% helix, 22% strand	P08238

Ligands and binding sites

83S · 5-Hydroxy-4-(isoindoline-2-carbonyl)-2-isopropylbenzaldehyde · ligand · 4 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, B, C

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

Pockets

6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	990	0.74	0.77	66	empty
2	804	0.68	0.75	70	GOL
3	284	0.64	0.81	33	83S, DMS
4	256	0.64	0.81	27	83S, DMS
5	223	0.61	0.81	24	83S, DMS

Interfaces

4 interfaces between chains.

A–B · 789 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 618 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 285 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 70 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5UC4 · Hsp90b N-terminal domain with inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
P08238 · AlphaFold monomer V2.0 prediction for heat shock protein HSP 90-beta (P08238) · a predicted model of the same protein · chain B against A, TM-score 0.81

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 P08238
Elsewhere: RCSB PDB 5UC4 · PDBe 5UC4 · UniProt P08238

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