MolNFT v1 · #123898 · protein
Allosteric inhibition of kidney isoform of glutaminase
5JYO · Glutaminase kidney isoform, mitochondrial: “Allosteric inhibition of kidney isoform of glutaminase”. X-ray diffraction, 1 ligand (63J), 16 pockets (best druggability 0.80). MolNFT v1 #123898 on GenesisL1: 3D structure, binding sites…
- PDB
- 5JYO
- Type
- protein
- Length
- 2,489 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaminase kidney isoform, mitochondrial
- EC
- 3.5.1.2
- UniProt
- O94925
- Ligands
- 63J
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B, E, F, G, H | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 311 | 48% helix, 14% strand | O94925 |
| A | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 312 | 48% helix, 13% strand | O94925 |
| C | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 311 | 48% helix, 14% strand | O94925 |
Ligands and binding sites
- 63J · 2-(pyridin-2-yl)-N-(5-{4-[6-({[3-(trifluoromethoxy)phenyl]acetyl}amino)pyridazin-3-yl]butyl}-1,3,4-thiadiazol-2-yl)acetamide · ligand · 4 copies · chains D, E, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.80 | 0.81 | 118 | empty |
| 2 | 937 | 0.79 | 0.81 | 113 | empty |
| 3 | 191 | 0.65 | 0.84 | 54 | empty |
| 4 | 124 | 0.64 | 0.87 | 29 | empty |
| 5 | 384 | 0.63 | 0.78 | 41 | empty |
Interfaces
8 interfaces between chains.
- B–E · 1118 Ų buried · 11 hydrogen bonds · protein-protein
- D–C · 1102 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 653 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 634 Ų buried · 2 hydrogen bonds · protein-protein
- E–G · 513 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5JYO · Allosteric inhibition of Kidney Isoform of Glutaminase · the same entry in another collection · chain H against H, TM-score 1.00
- O94925 · AlphaFold monomer V2.0 prediction for glutaminase kidney isoform, mitochondrial (O94925) · a predicted model of the same protein · chain C 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 O94925
- Elsewhere: RCSB PDB 5JYO · PDBe 5JYO · UniProt O94925
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