MolNFT v1 · #119844 · protein
Crystal structure of novel inhibitor bound with HSP90
5GGZ · Heat shock protein HSP 90-alpha: “Crystal structure of novel inhibitor bound with HSP90”. X-ray diffraction, 1 ligand (6TN), 9 pockets (best druggability 0.88). MolNFT v1 #119844 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5GGZ
- Type
- protein
- Length
- 837 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock protein HSP 90-alpha
- UniProt
- P07900
- Ligands
- 6TN
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Heat shock protein HSP 90-alpha | protein | 209 | 44% helix, 22% strand | P07900 |
| D | Heat shock protein HSP 90-alpha | protein | 210 | 44% helix, 22% strand | P07900 |
Ligands and binding sites
- 6TN · [2,4-bis(oxidanyl)-5-propan-2-yl-phenyl]-(2-ethoxy-7,8-dihydro-5~{H}-pyrido[4,3-d]pyrimidin-6-yl)methanone · ligand · 4 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.88 | 0.89 | 91 | 6TN |
| 2 | 1032 | 0.88 | 0.89 | 100 | 6TN |
| 3 | 444 | 0.62 | 0.76 | 55 | empty |
| 4 | 123 | 0.49 | 0.80 | 24 | empty |
| 5 | 81 | 0.34 | 0.74 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1081 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1067 Ų buried · 10 hydrogen bonds · protein-protein
- D–C · 394 Ų buried · 7 hydrogen bonds · protein-protein
- B–A · 381 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5GGZ · Crystal structure of novel inhibitor bound with Hsp90 · the same entry in another collection · chain B against B, TM-score 1.00
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 P07900
- Elsewhere: RCSB PDB 5GGZ · PDBe 5GGZ · UniProt P07900
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