Research workbench
Design and optimization of biaryl ether aryl sulfonamides as selective inhibitors of NAV1.7: discovery of clinical candidate pf-05089771
Analyse Design and optimization of biaryl ether aryl sulfonamides as selective… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K7K
- Type
- protein
- Length
- 455 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2C9
- EC
- 1.14.13.80
- UniProt
- P11712
- Ligands
- HEM, 6RJ
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2C9 (EC 1.14.13.80) | protein | 455 | 49% helix, 10% strand | P11712 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- 6RJ · 4-[4-chloranyl-2-(1~{H}-pyrazol-4-yl)phenoxy]-3-cyano-~{N}-(1,3-thiazol-2-yl)benzenesulfonamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.87 | 0.88 | 96 | HEM, 6RJ |
| 2 | 137 | 0.46 | 0.77 | 30 | empty |
| 3 | 138 | 0.43 | 0.75 | 23 | empty |
| 4 | 66 | 0.35 | 0.77 | 13 | empty |
| 5 | 58 | 0.34 | 0.78 | 13 | empty |
Compared structures
- 5K7K · Design and Optimization of Biaryl Ether Aryl Sulfonamides as Selective Inhibitors of… · the same entry in another collection · chain A against A, TM-score 1.00
- P11712 · AlphaFold monomer V2.0 prediction for cytochrome P450 2C9 (P11712) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P11712
- Elsewhere: RCSB PDB 5K7K · PDBe 5K7K · UniProt P11712
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