Research workbench
C-src V281C kinase domain in complex with rao-IV-156
Analyse C-src V281C kinase domain in complex with rao-IV-156 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TEH
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src
- EC
- 2.7.10.2
- UniProt
- P00523
- Ligands
- S56
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 261 | 38% helix, 13% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 262 | 36% helix, 12% strand | P00523 |
Ligands and binding sites
- S56 · (2S)-3-[4-amino-7-(2-methoxyethyl)-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-cyano-N-(propan-2-yl)propanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.77 | 0.84 | 59 | S56 |
| 2 | 843 | 0.72 | 0.77 | 78 | S56 |
| 3 | 309 | 0.56 | 0.76 | 33 | empty |
| 4 | 50 | 0.28 | 0.75 | 14 | empty |
| 5 | 73 | 0.28 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 366 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5TEH · c-Src V281C kinase domain in complex with Rao-IV-156 · 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 P00523
- Elsewhere: RCSB PDB 5TEH · PDBe 5TEH · UniProt P00523
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