Research workbench
Trka jm-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(1- NAPHTHYL)UREA
Analyse Trka jm-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(1- NAPHTHYL)UREA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KMM
- Type
- protein
- Length
- 301 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
- 6UJ
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High affinity nerve growth factor receptor (EC 2.7.10.1) | protein | 301 | 40% helix, 18% strand | P04629 |
Ligands and binding sites
- 6UJ · 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-naphthalen-1-yl-urea · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.75 | 0.85 | 43 | 6UJ |
| 2 | 140 | 0.60 | 0.84 | 24 | empty |
Compared structures
- 5KMM · TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(1-naphthyl)urea · 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 5KMM · PDBe 5KMM · UniProt P04629
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