Research workbench
Protein farnesyltransferase complexed with bisubstrate ethylenediamine scaffold inhibitor 5
Analyse Protein farnesyltransferase complexed with bisubstrate ethylenediamine scaffold… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E37
- Type
- protein
- Length
- 725 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type- 1 subunit alpha; Protein…
- EC
- 2.5.1.58, 2.5.1.59
- UniProt
- P49354, P49356
- Ligands
- ED5, GLC, FRU, ZN
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type- 1 subunit alpha (EC 2.5.1.58, 2.5.1.59) | protein | 315 | 70% helix, 1% strand | P49354 |
| B | Protein farnesyltransferase subunit beta (EC 2.5.1.58) | protein | 410 | 51% helix, 7% strand | P49356 |
Ligands and binding sites
- ED5 · tert-butyl 4-({(2-{(4-cyanophenyl)[(1-methyl-1H-imidazol-5-yl)methyl]amino}ethyl)[(2-methylphenyl)sulfonyl]amino}methyl)piperidine-1-carboxylate · ligand · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains A, B
- FRU · beta-D-fructofuranose · sugar · chains A, B
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.83 | 0.84 | 121 | ED5 |
| 2 | 245 | 0.62 | 0.81 | 33 | empty |
| 3 | 243 | 0.53 | 0.76 | 32 | empty |
| 4 | 75 | 0.43 | 0.80 | 16 | empty |
| 5 | 112 | 0.42 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 3505 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 3E37 · Protein farnesyltransferase complexed with bisubstrate ethylenediamine scaffold inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P49356 · AlphaFold monomer V2.0 prediction for protein farnesyltransferase subunit beta (P49356) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P49354 · AlphaFold monomer V2.0 prediction for protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERAS… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P49354
- Every structure of UniProt P49356
- Elsewhere: RCSB PDB 3E37 · PDBe 3E37 · UniProt P49354 · UniProt P49356
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