Research workbench
Crystal structure of trk-a in complex with the pan-trk kinase inhibitor, compound 19.
Analyse Crystal structure of trk-a in complex with the pan-trk kinase inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DKI
- Type
- protein
- Length
- 279 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
- 22L, GOD
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High affinity nerve growth factor receptor (EC 2.7.10.1) | protein | 279 | 42% helix, 18% strand | P04629 |
Ligands and binding sites
- 22L · 5-phenylthieno[2,3-d]pyrimidin-4(3H)-one · ligand · chains A
- GOD · 6-amino-5-{[(3S)-4,4-difluoro-1-{[4-(trifluoromethoxy) phenyl]acetyl}pyrrolidin-3-yl]oxy}-N-methylpyridine-3-carboxamide · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.72 | 0.81 | 51 | GOD |
| 2 | 103 | 0.39 | 0.76 | 23 | empty |
| 3 | 74 | 0.33 | 0.74 | 14 | empty |
Compared structures
- 6DKI · Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 19. · 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 P04629
- Elsewhere: RCSB PDB 6DKI · PDBe 6DKI · UniProt P04629
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