Research workbench
Trk-a in complex with ligand 1A
Analyse Trk-a in complex with ligand 1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PMB
- Type
- protein
- Length
- 288 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
- OQM
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High affinity nerve growth factor receptor (EC 2.7.10.1) | protein | 288 | 41% helix, 18% strand | P04629 |
Ligands and binding sites
- OQM · 2-[5,7-dimethyl-2-(pyridin-3-yl)[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]-N-[3-(trifluoromethyl) phenyl]acetamide · 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 | 620 | 0.74 | 0.80 | 60 | OQM |
| 2 | 78 | 0.33 | 0.74 | 22 | empty |
| 3 | 59 | 0.28 | 0.73 | 13 | empty |
Compared structures
- 6PMB · TRK-A IN COMPLEX WITH LIGAND 1a · 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 6PMB · PDBe 6PMB · UniProt P04629
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