Research workbench
Crystal structure of glutaminase C in complex with inhibitor cb-839
Analyse Crystal structure of glutaminase C in complex with inhibitor cb-839 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HL1
- Type
- protein
- Length
- 1,620 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
- 63J
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 404 | 50% helix, 11% strand | O94925 |
| B | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 410 | 49% helix, 11% strand | O94925 |
| C | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 404 | 49% helix, 11% strand | O94925 |
| D | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 402 | 50% helix, 10% 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 · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.87 | 0.88 | 125 | 63J |
| 2 | 1156 | 0.79 | 0.80 | 124 | empty |
| 3 | 399 | 0.71 | 0.82 | 50 | empty |
| 4 | 426 | 0.70 | 0.81 | 47 | empty |
| 5 | 125 | 0.48 | 0.79 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2023 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1968 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 640 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 615 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 44 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HL1 · Crystal structure of glutaminase C in complex with inhibitor CB-839 · 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 5HL1 · PDBe 5HL1 · UniProt O94925
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