Research workbench
C-src kinase domain in complex with small molecule inhibitor
Analyse C-src kinase domain in complex with small molecule inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F6X
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- 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
- IHH
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 264 | 42% helix, 16% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 267 | 40% helix, 17% strand | P00523 |
| C | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 265 | 40% helix, 17% strand | P00523 |
| D | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 267 | 40% helix, 17% strand | P00523 |
Ligands and binding sites
- IHH · [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl) amino]quinazolin-2-yl}amino)phenyl]acetonitrile · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.75 | 0.78 | 94 | IHH |
| 2 | 612 | 0.75 | 0.81 | 65 | IHH |
| 3 | 369 | 0.63 | 0.78 | 40 | IHH |
| 4 | 315 | 0.62 | 0.79 | 40 | IHH |
| 5 | 468 | 0.60 | 0.74 | 48 | empty |
Interfaces
5 interfaces between chains.
- A–C · 502 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 449 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 419 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 379 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 78 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3F6X · c-Src kinase domain in complex with small molecule inhibitor · 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 3F6X · PDBe 3F6X · UniProt P00523
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