MolNFT v1 · #186714 · protein
Discovery of an anion-dependent farnesyltransferase inhibitor from a phenotypic screen
7RN5 · Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type…: “Discovery of an anion-dependent farnesyltransferase inhibitor from a phenotypic screen”. X-ray diffraction, 5 ligands (ACE, 60I, PPV), 13 pockets (best druggability…
- PDB
- 7RN5
- Type
- protein
- Length
- 717 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
- Q04631, Q02293
- Ligands
- ACE, 60I, PPV, ZN, MG
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 60% 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 | 313 | 69% helix, 1% strand | Q04631 |
| B | Protein farnesyltransferase subunit beta (EC 2.5.1.58) | protein | 404 | 52% helix, 6% strand | Q02293 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- 60I · [4-[[3-(2,2-dimethylpropyl)-1~{H}-benzimidazol-2-yl]methyl]piperazin-1-yl]-(1,3,5-trimethylpyrazol-4-yl)methanone · ligand · chains A, B
- PPV · Pyrophosphate · ligand · chains A, B
- ZN · Zinc ion · metal · chains B
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.78 | 0.80 | 76 | 60I, ZN, MG, PPV |
| 2 | 92 | 0.75 | 0.97 | 23 | empty |
| 3 | 196 | 0.74 | 0.90 | 33 | empty |
| 4 | 270 | 0.56 | 0.78 | 38 | empty |
| 5 | 76 | 0.50 | 0.84 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3546 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 7RN5 · Discovery of an Anion-Dependent Farnesyltransferase Inhibitor from a Phenotypic Screen · the same entry in another collection · chain A against A, TM-score 1.00
- Q04631 · AlphaFold monomer V2.0 prediction for protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERAS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q02293 · AlphaFold monomer V2.0 prediction for protein farnesyltransferase subunit beta (Q02293) · a predicted model of the same protein · chain B 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 Q04631
- Every structure of UniProt Q02293
- Elsewhere: RCSB PDB 7RN5 · PDBe 7RN5 · UniProt Q04631 · UniProt Q02293
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