Research workbench
In meso full-length rat kmo in complex with a pyrazoyl benzoic acid inhibitor
Analyse In meso full-length rat kmo in complex with a pyrazoyl benzoic acid inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LKD
- Type
- protein
- Length
- 848 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kynurenine 3-monooxygenase
- EC
- 1.14.13.9
- UniProt
- O88867
- Ligands
- FAD, EGO, SO4, CL
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kynurenine 3-monooxygenase (EC 1.14.13.9) | protein | 427 | 43% 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
- EGO · 5-[5-(4-chloranyl-3-fluoranyl-phenyl)-4-methyl-pyrazol-1-yl]-2-phenylmethoxy-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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.85 | 0.86 | 91 | FAD, EGO, CL |
| 2 | 927 | 0.84 | 0.85 | 100 | FAD, EGO, CL |
| 3 | 122 | 0.56 | 0.83 | 23 | empty |
| 4 | 84 | 0.47 | 0.81 | 16 | empty |
| 5 | 87 | 0.41 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 647 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6LKD · in meso full-length rat KMO in complex with a pyrazoyl benzoic acid inhibitor · 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 6LKD · PDBe 6LKD · UniProt O88867
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