MolNFT v1 · #116021 · protein
Kinase domain of csrc in complex with RL236
5D10 · Proto-oncogene tyrosine-protein kinase src: “Kinase domain of csrc in complex with RL236”. X-ray diffraction, 1 ligand (563), 5 pockets (best druggability 0.62). MolNFT v1 #116021 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5D10
- Type
- protein
- Length
- 495 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
- 563
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 248 | 43% helix, 16% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 247 | 41% helix, 16% strand | P00523 |
Ligands and binding sites
- 563 · N-[4-({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
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 | 395 | 0.62 | 0.77 | 48 | 563 |
| 2 | 318 | 0.61 | 0.78 | 32 | 563 |
| 3 | 362 | 0.60 | 0.77 | 45 | empty |
| 4 | 75 | 0.33 | 0.75 | 18 | empty |
| 5 | 58 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 375 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5D10 · Kinase domain of cSrc in complex with RL236 · 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 5D10 · PDBe 5D10 · UniProt P00523
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