MolNFT v1 · #146552 · protein
Crystal structure of trk-a in complex with the pan-trk kinase inhibitor, compound 3.
6DKW · Tyrosine-protein kinase receptor: “Crystal structure of trk-a in complex with the pan-trk kinase inhibitor, compound 3.”. X-ray diffraction, 1 ligand (GXA), 5 pockets (best druggability 0.75). MolNFT v1 #146552 on GenesisL1: 3D…
- PDB
- 6DKW
- Type
- protein
- Length
- 553 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase receptor
- EC
- 2.7.10.1
- UniProt
- J3KP20
- Ligands
- GXA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase receptor (EC 2.7.10.1) | protein | 284 | 40% helix, 15% strand | J3KP20 |
| B | Tyrosine-protein kinase receptor (EC 2.7.10.1) | protein | 269 | 40% helix, 16% strand | J3KP20 |
Ligands and binding sites
- GXA · 5-(1-methyl-1H-imidazol-4-yl)-2-[(1-{[4-(trifluoromethoxy)phenyl]acetyl}piperidin-4-yl) oxy]benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.75 | 0.80 | 73 | GXA |
| 2 | 409 | 0.67 | 0.80 | 41 | GXA |
| 3 | 202 | 0.53 | 0.78 | 24 | empty |
| 4 | 88 | 0.32 | 0.73 | 17 | empty |
| 5 | 51 | 0.28 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 767 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6DKW · Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 3. · 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 J3KP20
- Elsewhere: RCSB PDB 6DKW · PDBe 6DKW · UniProt J3KP20
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