MolNFT v1 · #134326 · protein
C-src kinase domain in complex with rao-IV-151
5T0P · Proto-oncogene tyrosine-protein kinase src: “C-src kinase domain in complex with rao-IV-151”. X-ray diffraction, 1 ligand (73A), 6 pockets (best druggability 0.71). MolNFT v1 #134326 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5T0P
- Type
- protein
- Length
- 527 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
- 73A
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 264 | 38% helix, 16% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 263 | 38% helix, 16% strand | P00523 |
Ligands and binding sites
- 73A · (2E)-3-[4-amino-5-(4-chlorophenyl)-7-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl]-2-cyano-N-(propan-2-yl)prop-2-enamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.71 | 0.76 | 87 | 73A |
| 2 | 222 | 0.61 | 0.81 | 31 | 73A |
| 3 | 368 | 0.58 | 0.76 | 45 | empty |
| 4 | 68 | 0.44 | 0.82 | 14 | empty |
| 5 | 54 | 0.44 | 0.84 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 401 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5T0P · c-Src kinase domain in complex with Rao-IV-151 · 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 5T0P · PDBe 5T0P · UniProt P00523
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