MolNFT v1 · #68976 · protein
Crystal structure of human liver fbpase in complex with tricyclic inhibitor 10B
3KC0 · Fructose-1,6-bisphosphatase 1: “Crystal structure of human liver fbpase in complex with tricyclic inhibitor 10B”. X-ray diffraction, 1 ligand (2T5), 20 pockets (best druggability 0.85). MolNFT v1 #68976 on GenesisL1: 3D structure…
- PDB
- 3KC0
- Type
- protein
- Length
- 1,273 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-1,6-bisphosphatase 1
- EC
- 3.1.3.11
- UniProt
- P09467
- Ligands
- 2T5
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 319 | 38% helix, 24% strand | P09467 |
| B, C, D | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 318 | 39% helix, 25% strand | P09467 |
Ligands and binding sites
- 2T5 · [(8H-indeno[1,2-d][1,3]thiazol-4-yloxy)methyl]phosphonic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.85 | 0.87 | 94 | empty |
| 2 | 62 | 0.73 | 0.99 | 31 | empty |
| 3 | 60 | 0.72 | 0.98 | 30 | empty |
| 4 | 113 | 0.56 | 0.84 | 31 | empty |
| 5 | 190 | 0.54 | 0.79 | 36 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2383 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2372 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1145 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1124 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 440 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3KC0 · Crystal structure of human liver FBPase in complex with tricyclic inhibitor 10b · the same entry in another collection · chain D against D, TM-score 1.00
- P09467 · AlphaFold monomer V2.0 prediction for fructose-1,6-bisphosphatase 1 (P09467) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P09467
- Elsewhere: RCSB PDB 3KC0 · PDBe 3KC0 · UniProt P09467
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