Research workbench
in meso full-length rat KMO in complex with an inhibitor identified via DNA-encoded chemical library screening
Analyse in meso full-length rat KMO in complex with an inhibitor identified via… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LKE
- Type
- protein
- Length
- 849 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Rattus norvegicus
- Molecule
- Kynurenine 3-monooxygenase
- EC
- 1.14.13.9
- UniProt
- O88867
- Ligands
- FAD, EGU, SO4, CL
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · resolution 3 · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kynurenine 3-monooxygenase (EC 1.14.13.9) | protein | 428 | 44% helix, 23% strand | O88867 |
| B | Kynurenine 3-monooxygenase (EC 1.14.13.9) | protein | 421 | 41% helix, 26% strand | O88867 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- EGU · 4-chloranyl-2-[[5-chloranyl-2-(5-methoxy-1,3-dihydroisoindol-2-yl)-1,3-thiazol-4-yl]carbonyl-methyl-amino]-5-fluoranyl-benzoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.86 | 0.87 | 92 | FAD, CL, EGU |
| 2 | 967 | 0.84 | 0.85 | 93 | FAD, CL, EGU |
| 3 | 148 | 0.54 | 0.81 | 23 | empty |
| 4 | 109 | 0.51 | 0.81 | 21 | empty |
| 5 | 69 | 0.40 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 669 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6LKE · In meso full-length rat kmo in complex with an inhibitor identified via DNA-encoded… · the same entry in another collection · chain A against A, TM-score 1.00
- O88867 · AlphaFold monomer V2.0 prediction for kynurenine 3-monooxygenase (O88867) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O88867
- Elsewhere: RCSB PDB 6LKE · PDBe 6LKE · UniProt O88867
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