MolNFT v1 · #175425 · protein
Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase mer in complex with azd-7762
7CQE: “Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase mer in complex with…”. X-ray diffraction, 2 ligands (YDJ, CL), 4 pockets (best druggability 0.64). MolNFT v1 #175425 on GenesisL1: 3D structure…
- PDB
- 7CQE
- Type
- protein
- Length
- 492 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase mer
- EC
- 2.7.10.1
- UniProt
- Q12866
- Ligands
- YDJ, CL
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 253 | 41% helix, 18% strand | Q12866 |
| C | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 239 | 42% helix, 16% strand | Q12866 |
Ligands and binding sites
- YDJ · 5-(3-fluorophenyl)-N-[(3S)-3-piperidyl]-3-ureido-thiophene-2-carboxamide · ligand · 2 copies · chains A, C
- CL · Chloride ion · ion · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.64 | 0.76 | 67 | YDJ |
| 2 | 254 | 0.59 | 0.78 | 27 | CL, YDJ |
| 3 | 134 | 0.53 | 0.81 | 22 | empty |
| 4 | 78 | 0.50 | 0.84 | 23 | empty |
Interfaces
1 interface between chains.
- A–C · 1065 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7CQE · Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase… · 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 Q12866
- Elsewhere: RCSB PDB 7CQE · PDBe 7CQE · UniProt Q12866
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