Research workbench
Crystal structure of compound 8 bound to TAK1-tab
Analyse Crystal structure of compound 8 bound to TAK1-tab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YIY
- Type
- protein
- Length
- 293 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase kinase kinase 7, TGF-beta- activated kinase 1 and…
- EC
- 2.7.11.25
- UniProt
- O43318, Q15750
- Ligands
- YIY
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase 7, TGF-beta- activated kinase 1 and MAP3K7-binding protein 1 (EC 2.7.11.25) | protein | 293 | 39% helix, 17% strand | O43318, Q15750 |
Ligands and binding sites
- YIY · (1E)-1-[5-tert-butyl-2-(3-fluorophenyl)-1H-pyrazol-3-ylidene]-3-(4-pyridin-3-yloxyphenyl)urea · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.70 | 0.82 | 40 | YIY |
| 2 | 117 | 0.42 | 0.76 | 24 | empty |
| 3 | 62 | 0.30 | 0.74 | 16 | empty |
Compared structures
- 2YIY · Crystal structure of compound 8 bound to TAK1-TAB · the same entry in another collection · chain A against A, TM-score 1.00
- O43318 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase kinase kinase 7… · a predicted model of the same protein · chain A against A, TM-score 0.91
- Q15750 · AlphaFold monomer V2.0 prediction for TGF-beta-activated kinase 1 and MAP3K7-binding… · a predicted model of the same protein · chain A against A, TM-score 0.31
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 O43318
- Every structure of UniProt Q15750
- Elsewhere: RCSB PDB 2YIY · PDBe 2YIY · UniProt O43318 · UniProt Q15750
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