MolNFT v1 · #135888 · protein

HSP90B N-terminal domain with inhibitors

5UCH · Heat shock protein HSP 90-beta: “HSP90B N-terminal domain with inhibitors”. X-ray diffraction, 1 ligand (871), 8 pockets (best druggability 0.74). MolNFT v1 #135888 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5UCH
Type: protein
Length: 853 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: 871
Pockets: 8 · best druggability 0.74

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Heat shock protein HSP 90-beta	protein	219	42% helix, 23% strand	P08238
B	Heat shock protein HSP 90-beta	protein	208	43% helix, 24% strand	P08238
D	Heat shock protein HSP 90-beta	protein	207	44% helix, 23% strand	P08238

Ligands and binding sites

871 · 2-(5-Hydroxy-4-(isoindoline-2-carbonyl)-2-isopropylphenyl)acetonitrile · 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

8 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	930	0.74	0.77	73	empty
2	673	0.66	0.75	61	GOL
3	256	0.65	0.82	33	871, DMS
4	357	0.63	0.78	38	871, DMS
5	240	0.63	0.82	32	871, DMS

Interfaces

5 interfaces between chains.

A–B · 767 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 624 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 323 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 39 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 13 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5UCH · 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 D 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 5UCH · PDBe 5UCH · UniProt P08238

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