MolNFT v1 · #148110 · protein
Crystal structure of rhodesain in complex with a macrolactam inhibitor
6EX8 · Cysteine protease: “Crystal structure of rhodesain in complex with a macrolactam inhibitor”. X-ray diffraction, 1 ligand (C2K), 5 pockets (best druggability 0.78). MolNFT v1 #148110 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6EX8
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine protease
- UniProt
- Q95PM0
- Ligands
- C2K
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cysteine protease | protein | 217 | 26% helix, 23% strand | Q95PM0 |
Ligands and binding sites
- C2K · (3~{S})-~{N}-[1-(aminomethyl)cyclopropyl]-19-chloranyl-5-oxidanylidene-9-(trifluoromethyl)-12,17-dioxa-4-azatricyclo[16.2.2.0^{6,11}]docosa-1(20),6(11),7,9,18,21-hexaene-3-carboxamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.78 | 0.85 | 60 | EDO |
| 2 | 94 | 0.33 | 0.73 | 23 | empty |
| 3 | 65 | 0.33 | 0.77 | 13 | empty |
| 4 | 61 | 0.33 | 0.76 | 15 | empty |
| 5 | 52 | 0.28 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 605 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified, 1 covalent (disulfide, oxidation, covalent ligand).
Compared structures
- 6EX8 · Crystal Structure of Rhodesain in complex with a Macrolactam Inhibitor · the same entry in another collection · chain A against A, 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 Q95PM0
- Elsewhere: RCSB PDB 6EX8 · PDBe 6EX8 · UniProt Q95PM0
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