Research workbench
Optimization of tead P-site binding fragment hit into in vivo active lead msc-4106
Analyse Optimization of tead P-site binding fragment hit into in vivo active lead… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZJP
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional enhancer factor tef-1
- UniProt
- P28347
- Ligands
- JJU, SO4
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional enhancer factor tef-1 | protein | 215 | 17% helix, 51% strand | P28347 |
| B | Transcriptional enhancer factor tef-1 | protein | 213 | 17% helix, 53% strand | P28347 |
Ligands and binding sites
- JJU · 2-methyl-4-[4-(trifluoromethyl)phenyl]pyrazolo[3,4-b]indole-7-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.83 | 0.95 | 37 | JJU |
| 2 | 206 | 0.83 | 0.96 | 37 | JJU |
| 3 | 500 | 0.70 | 0.80 | 44 | SO4 |
| 4 | 66 | 0.59 | 0.90 | 18 | empty |
| 5 | 99 | 0.39 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 763 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7ZJP · Optimization of TEAD P-Site Binding Fragment Hit into In Vivo Active Lead MSC-4106 · the same entry in another collection · chain A against A, TM-score 1.00
- P28347 · AlphaFold monomer V2.0 prediction for transcriptional enhancer factor tef-1 (P28347) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P28347
- Elsewhere: RCSB PDB 7ZJP · PDBe 7ZJP · UniProt P28347
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