Research workbench
Discovery of a dual inhibitor of NQO1 and GSTP1 for treating malignant glioblastoma
Analyse Discovery of a dual inhibitor of NQO1 and GSTP1 for treating malignant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LLC
- Type
- protein
- Length
- 3,250 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H dehydrogenase [quinone] 1
- EC
- 1.6.5.2
- UniProt
- P15559
- Ligands
- FAD, EHL, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2) | protein | 272 | 40% helix, 17% strand | P15559 |
| B, C, E, F, K, L | NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2) | protein | 271 | 40% helix, 16% strand | P15559 |
| G, H, I, J | NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2) | protein | 270 | 39% helix, 16% strand | P15559 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 12 copies · chains A, D, B, F, C, E, G, H, I, J, K, L
- EHL · 5-methyl-N-(5-nitro-1,3-thiazol-2-yl)-3-phenyl-1,2-oxazole-4-carboxamide · ligand · 8 copies · chains A, D, B, F, E, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 4 copies · chains A, D, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.84 | 0.87 | 83 | empty |
| 2 | 1005 | 0.81 | 0.82 | 105 | FAD |
| 3 | 941 | 0.80 | 0.82 | 85 | empty |
| 4 | 529 | 0.80 | 0.86 | 50 | FAD |
| 5 | 558 | 0.79 | 0.85 | 57 | EHL, FAD |
Interfaces
15 interfaces between chains.
- K–L · 2792 Ų buried · 34 hydrogen bonds · protein-protein
- I–J · 2776 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 2762 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 2757 Ų buried · 37 hydrogen bonds · protein-protein
- B–F · 2749 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6LLC · Discovery of A Dual Inhibitor of NQO1 and GSTP1 for Treating Malignant Glioblastoma · the same entry in another collection · chain L against L, TM-score 1.00
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 P15559
- Elsewhere: RCSB PDB 6LLC · PDBe 6LLC · UniProt P15559
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