MolNFT v1 · #135890 · protein

HSP90B N-terminal domain with inhibitors

5UCJ · Heat shock protein HSP 90-beta: “HSP90B N-terminal domain with inhibitors”. X-ray diffraction, 1 ligand (KU3), 6 pockets (best druggability 0.82). MolNFT v1 #135890 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5UCJ
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: KU3
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heat shock protein HSP 90-beta	protein	218	43% helix, 22% strand	P08238
B	Heat shock protein HSP 90-beta	protein	219	42% helix, 22% strand	P08238
C, D	Heat shock protein HSP 90-beta	protein	208	44% helix, 23% strand	P08238

Ligands and binding sites

KU3 · (5-fluoroisoindolin-2-yl)(4-hydroxy-5-isopropylbenzo[d]isoxazol-7-yl)methanone · ligand · 4 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1034	0.82	0.84	113	KU3, DMS
2	781	0.75	0.80	78	KU3, DMS
3	281	0.62	0.80	28	KU3, DMS
4	236	0.61	0.80	24	KU3, DMS
5	183	0.48	0.76	30	empty

Interfaces

4 interfaces between chains.

B–D · 727 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 659 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 450 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 288 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5UCJ · 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 C 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 5UCJ · PDBe 5UCJ · UniProt P08238

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