Research workbench
Discovery of C-imidazole azaheptapyridine fpt inhibitors
Analyse Discovery of C-imidazole azaheptapyridine fpt inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KSQ
- Type
- protein
- Length
- 718 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyltransferase, caax box, alpha; Protein farnesyltransferase subunit beta
- EC
- 2.5.1.58
- UniProt
- Q5RKJ4, Q02293
- Ligands
- FPP, Z96, MG, ZN
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyltransferase, caax box, alpha (EC 2.5.1.58) | protein | 315 | 68% helix, 1% strand | Q5RKJ4 |
| B | Protein farnesyltransferase subunit beta (EC 2.5.1.58) | protein | 403 | 52% helix, 7% strand | Q02293 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A, B
- Z96 · tert-butyl 4-{(11S)-8-chloro-6-[(R)-hydroxy(1-methyl-1H-imidazol-5-yl)methyl]-11H-benzo[5,6]cyclohepta[1,2-b]pyridin-11-yl}piperazine-1-carboxylate · ligand · chains A, B
- MG · Magnesium ion · metal · 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.77 | 0.79 | 74 | ZN, FPP, Z96 |
| 2 | 239 | 0.73 | 0.88 | 43 | empty |
| 3 | 78 | 0.73 | 0.96 | 25 | empty |
| 4 | 206 | 0.61 | 0.82 | 25 | empty |
| 5 | 292 | 0.56 | 0.77 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 3481 Ų buried · 68 hydrogen bonds · protein-protein
Compared structures
- 3KSQ · Discovery of C-Imidazole Azaheptapyridine FPT Inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- 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 Q5RKJ4
- Every structure of UniProt Q02293
- Elsewhere: RCSB PDB 3KSQ · PDBe 3KSQ · UniProt Q5RKJ4 · UniProt Q02293
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