Research workbench
Focal adhesion kinase catalytic domain in complex with 5-{4-[(pyridin- 3-ylmethyl)-amino]-5-trifluoromethyl-pyrimidin-2-ylamino}-1,3- dihydro-indol-2-one
Analyse Focal adhesion kinase catalytic domain in complex with 5-{4-[(pyridin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YVS
- Type
- protein
- Length
- 1,025 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Focal adhesion kinase 1
- EC
- 2.7.10.2
- UniProt
- Q05397
- Ligands
- PVT, SO4
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Focal adhesion kinase 1 (EC 2.7.10.2) | protein | 260 | 42% helix, 18% strand | Q05397 |
| B | Focal adhesion kinase 1 (EC 2.7.10.2) | protein | 254 | 45% helix, 18% strand | Q05397 |
| C | Focal adhesion kinase 1 (EC 2.7.10.2) | protein | 254 | 44% helix, 18% strand | Q05397 |
| D | Focal adhesion kinase 1 (EC 2.7.10.2) | protein | 257 | 46% helix, 18% strand | Q05397 |
Ligands and binding sites
- PVT · 5-[[4-(pyridin-3-ylmethylamino)-5-(trifluoromethyl) pyrimidin-2-yl]amino]-1,3-dihydroindol-2-one · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.70 | 0.78 | 65 | PVT |
| 2 | 423 | 0.65 | 0.78 | 42 | empty |
| 3 | 305 | 0.64 | 0.81 | 33 | PVT |
| 4 | 301 | 0.61 | 0.79 | 34 | PVT |
| 5 | 264 | 0.58 | 0.78 | 32 | PVT |
Interfaces
3 interfaces between chains.
- A–D · 770 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 351 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 300 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 Q05397
- Elsewhere: RCSB PDB 6YVS · PDBe 6YVS · UniProt Q05397
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