Research workbench
Crystal structure of human gac in complex with inhibitor UPGL00012
Analyse Crystal structure of human gac in complex with inhibitor UPGL00012 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UKB
- Type
- protein
- Length
- 1,638 residues
- Chains
- 4
- 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
- Q9V
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 409 | 48% helix, 12% strand | O94925 |
| C, D | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 410 | 48% helix, 11% strand | O94925 |
Ligands and binding sites
- Q9V · N-[5-(4-{[5-(acetylamino)-1,3,4-thiadiazol-2-yl]oxy}piperidin-1-yl)-1,3,4-thiadiazol-2-yl]acetamide · ligand · 2 copies · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.79 | 0.83 | 106 | empty |
| 2 | 1191 | 0.75 | 0.77 | 84 | empty |
| 3 | 448 | 0.69 | 0.80 | 44 | empty |
| 4 | 429 | 0.67 | 0.79 | 44 | empty |
| 5 | 112 | 0.66 | 0.89 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1961 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 791 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 199 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 118 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6UKB · Crystal structure of human GAC in complex with inhibitor UPGL00012 · the same entry in another collection · chain D against D, TM-score 1.00
- O94925 · AlphaFold monomer V2.0 prediction for glutaminase kidney isoform, mitochondrial (O94925) · 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 O94925
- Elsewhere: RCSB PDB 6UKB · PDBe 6UKB · UniProt O94925
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