MolNFT v1 · #85836 · protein
Human trka in complex with the inhibitor az-23
4AOJ · High affinity nerve growth factor receptor: “Human trka in complex with the inhibitor az-23”. X-ray diffraction, 2 ligands (V4Z, ZN), 11 pockets (best druggability 0.70). MolNFT v1 #85836 on GenesisL1: 3D structure, binding sites…
- PDB
- 4AOJ
- Type
- protein
- Length
- 779 residues
- Chains
- 3
- 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
- V4Z, ZN
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 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 | 260 | 39% helix, 18% strand | P04629 |
| B | High affinity nerve growth factor receptor (EC 2.7.10.1) | protein | 258 | 40% helix, 18% strand | P04629 |
| C | High affinity nerve growth factor receptor (EC 2.7.10.1) | protein | 261 | 40% helix, 19% strand | P04629 |
Ligands and binding sites
- V4Z · 5-chloranyl-N2-[(1S)-1-(5-fluoranylpyridin-2-yl)ethyl]-N4-(3-propan-2-yloxy-1H-pyrazol-5-yl)pyrimidine-2,4-diamine · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.70 | 0.79 | 60 | V4Z |
| 2 | 281 | 0.67 | 0.82 | 32 | V4Z |
| 3 | 254 | 0.65 | 0.82 | 31 | V4Z |
| 4 | 185 | 0.50 | 0.76 | 26 | empty |
| 5 | 140 | 0.48 | 0.78 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 785 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 771 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4AOJ · Human TrkA in complex with the inhibitor AZ-23 · 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 B against A, TM-score 0.98
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 4AOJ · PDBe 4AOJ · UniProt P04629
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