Research workbench
Trka jm-kinase with 2-fluoro-{N}-[2-(4-fluorophenyl)-6-methyl-3- pyridyl]-4-(TRIFLUOROMETHYL)BENZAMIDE
Analyse Trka jm-kinase with 2-fluoro-{N}-[2-(4-fluorophenyl)-6-methyl-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KMK
- Type
- protein
- Length
- 304 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity nerve growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P04629
- Ligands
- 6UG
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High affinity nerve growth factor receptor (EC 2.7.10.1) | protein | 304 | 38% helix, 18% strand | P04629 |
Ligands and binding sites
- 6UG · 2-fluoranyl-~{N}-[2-(4-fluorophenyl)-6-methyl-pyridin-3-yl]-4-(trifluoromethyl)benzamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.76 | 0.86 | 45 | 6UG |
| 2 | 136 | 0.56 | 0.82 | 24 | empty |
| 3 | 54 | 0.27 | 0.73 | 14 | empty |
Compared structures
- 5KMK · TrkA JM-kinase with 2-fluoro-{N}-[2-(4-fluorophenyl)-6-methyl-3-pyridyl]-4-(trifluoromethy… · the same entry in another collection · chain A against A, TM-score 1.00
- P04629 · AlphaFold monomer V2.0 prediction for high affinity nerve growth factor receptor (P04629) · 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 P04629
- Elsewhere: RCSB PDB 5KMK · PDBe 5KMK · UniProt P04629
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