Research workbench
Structure of the human quinone reductase 2 (NQO2) in complex with pacritinib
Analyse Structure of the human quinone reductase 2 (NQO2) in complex with pacritinib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LBZ
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosyldihydronicotinamide dehydrogenase [quinone]
- EC
- 1.10.5.1
- UniProt
- P16083
- Ligands
- FAD, 6T3, ZN, SO4
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribosyldihydronicotinamide dehydrogenase [quinone] (EC 1.10.5.1) | protein | 227 | 41% helix, 17% strand | P16083 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 6T3 · 11-(2-pyrrolidin-1-yl-ethoxy)-14,19-dioxa-5,7,26-triaza-tetracyclo[19.3.1.1(2,6).1(8,12)]heptacosa-1(25),2(26),3,5,8,10,12(27),16,21,23-decaene · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.77 | 0.83 | 42 | FAD, 6T3 |
| 2 | 615 | 0.76 | 0.82 | 44 | 6T3, FAD |
Interfaces
1 interface between chains.
- A–B · 1981 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5LBZ · Structure of the human qui reductase 2 (NQO2) in complex with pacritinib · the same entry in another collection · chain A against A, 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 P16083
- Elsewhere: RCSB PDB 5LBZ · PDBe 5LBZ · UniProt P16083
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