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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: 5UCI
Type: protein
Length: 852 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: 874
Pockets: 6 · best druggability 0.69

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	42% helix, 23% strand	P08238
B, D	Heat shock protein HSP 90-beta	protein	208	45% helix, 24% strand	P08238
C	Heat shock protein HSP 90-beta	protein	217	43% helix, 22% strand	P08238

Ligands and binding sites

874 · (2,4-dihydroxy-3-(hydroxymethyl)-5-isopropylphenyl) (isoindolin-2-yl)methanone · 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 B, C, D

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	804	0.69	0.76	69	GOL
2	745	0.69	0.76	60	empty
3	269	0.63	0.80	31	874, DMS
4	228	0.62	0.81	23	874, DMS
5	225	0.61	0.81	28	874, DMS

Interfaces

5 interfaces between chains.

A–B · 792 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 643 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 304 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 29 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 18 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5UCI · 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 0.82

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 5UCI · PDBe 5UCI · UniProt P08238

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