Research workbench
Focal adhesion kinase catalytic domain in complex with 4-{[4-{[(1R, 2R)-2-(DIMETHYLAMINO)CYCLOPENTYL]AMINO}-5-(TRIFLUOROMETHYL)PYRIMIDIN- 2-YL]AMINO}-N-methylbenzenesulfonamide
Analyse Focal adhesion kinase catalytic domain in complex with 4-{[4-{[(1R… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YVY
- Type
- protein
- Length
- 1,035 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
- P1E, SO4
- Pockets
- 11 · best druggability 0.68
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 | 265 | 42% helix, 19% strand | Q05397 |
| B | Focal adhesion kinase 1 (EC 2.7.10.2) | protein | 257 | 45% helix, 18% strand | Q05397 |
| C | Focal adhesion kinase 1 (EC 2.7.10.2) | protein | 258 | 45% helix, 18% strand | Q05397 |
| D | Focal adhesion kinase 1 (EC 2.7.10.2) | protein | 255 | 44% helix, 17% strand | Q05397 |
Ligands and binding sites
- P1E · 4-{[4-{[(1R,2R)-2-(dimethylamino)cyclopentyl]amino}-5-(trifluoromethyl)pyrimidin-2-yl]amino}-N-methylbenzenesulfonamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.68 | 0.77 | 66 | SO4 |
| 2 | 357 | 0.68 | 0.81 | 41 | P1E |
| 3 | 309 | 0.66 | 0.81 | 41 | P1E |
| 4 | 303 | 0.64 | 0.81 | 40 | P1E |
| 5 | 243 | 0.64 | 0.82 | 33 | empty |
Interfaces
4 interfaces between chains.
- B–C · 563 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 562 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 451 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 402 Ų buried · 3 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 6YVY · PDBe 6YVY · UniProt Q05397
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