MolNFT v1 · #103640 · protein
The structure of trka kinase bound to the inhibitor 1-cyclopropyl-1- [3-(1,3-thiazol-2-YL)BENZYL]-3-[4-(TRIFLUOROMETHOXY)PHENYL]UREA
4PMP · High affinity nerve growth factor receptor: “The structure of trka kinase bound to the inhibitor 1-cyclopropyl-1…”. X-ray diffraction, 2 ligands (31W, CL), 2 pockets (best druggability 0.73). MolNFT v1 #103640 on GenesisL1: 3D…
- PDB
- 4PMP
- Type
- protein
- Length
- 280 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
- 31W, CL
- Pockets
- 2 · best druggability 0.73
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 | 280 | 42% helix, 18% strand | P04629 |
Ligands and binding sites
- 31W · 1-cyclopropyl-1-[3-(1,3-thiazol-2-yl)benzyl]-3-[4-(trifluoromethoxy)phenyl]urea · ligand · chains A
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 3 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.73 | 0.80 | 61 | 31W |
| 2 | 59 | 0.28 | 0.74 | 21 | ACT |
Compared structures
- 4PMP · The structure of TrkA kinase bound to the inhibitor… · 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 0.96
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 4PMP · PDBe 4PMP · UniProt P04629
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