MolNFT v1 · #116022 · protein
Kinase domain of csrc in complex with RL235
5D11 · Proto-oncogene tyrosine-protein kinase src: “Kinase domain of csrc in complex with RL235”. X-ray diffraction, 1 ligand (56G), 3 pockets (best druggability 0.71). MolNFT v1 #116022 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5D11
- Type
- protein
- Length
- 509 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
- 56G
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 254 | 40% helix, 17% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 255 | 41% helix, 17% strand | P00523 |
Ligands and binding sites
- 56G · N-[3-({4-(4-methylpiperazin-1-yl)-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}oxy)phenyl]prop-2-enamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.71 | 0.76 | 98 | 56G |
| 2 | 365 | 0.60 | 0.77 | 42 | empty |
| 3 | 221 | 0.57 | 0.79 | 36 | 56G |
Interfaces
1 interface between chains.
- A–B · 364 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5D11 · Kinase domain of cSrc in complex with RL235 · 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 5D11 · PDBe 5D11 · UniProt P00523
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