MolNFT v1 · #32039 · protein
Structure of fpt bound to inhibitor SCH207736
2BED · Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type…: “Structure of fpt bound to inhibitor SCH207736”. X-ray diffraction, 3 ligands (FPP, 736, ZN), 8 pockets (best druggability 0.79). MolNFT v1 #32039 on GenesisL1: 3D…
- PDB
- 2BED
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type I alpha subunit; Protein…
- EC
- 2.5.1.58, 2.5.1.59
- UniProt
- Q04631, Q02293
- Ligands
- FPP, 736, ZN
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type I alpha subunit (EC 2.5.1.58, 2.5.1.59) | protein | 313 | 69% helix, 1% strand | Q04631 |
| B | Protein farnesyltransferase beta subunit (EC 2.5.1.58) | protein | 401 | 49% helix, 7% strand | Q02293 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A, B
- 736 · (11S)-8-chloro-11-[1-(methylsulfonyl)piperidin-4-yl]-6-piperazin-1-yl-11H-benzo[5,6]cyclohepta[1,2-b]pyridine · ligand · 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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.79 | 0.81 | 102 | FPP, 736 |
| 2 | 100 | 0.76 | 0.97 | 24 | empty |
| 3 | 224 | 0.64 | 0.83 | 28 | empty |
| 4 | 250 | 0.56 | 0.78 | 22 | empty |
| 5 | 79 | 0.50 | 0.84 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3442 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 2BED · Structure of FPT bound to inhibitor SCH207736 · 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 2BED · PDBe 2BED · UniProt Q04631 · UniProt Q02293
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