Research workbench
Crystal structure of CGD4-650 with compound BI2536
Analyse Crystal structure of CGD4-650 with compound BI2536 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MF9
- Type
- protein
- Length
- 253 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.037
- Source
- Cryptosporidium parvum (strain Iowa II)
- Molecule
- ZnKn (C2HC)+Athook+bromo domain protein, Taf250, transcription initiation factor IID
- UniProt
- Q5CQH9
- Ligands
- R78
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · resolution 2.037 · 2 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ZnKn (C2HC)+Athook+bromo domain protein, Taf250, transcription initiation factor IID | protein | 126 | 66% helix, 0% strand | Q5CQH9 |
| B | ZnKn (C2HC)+Athook+bromo domain protein, Taf250, transcription initiation factor IID | protein | 127 | 67% helix, 0% strand | Q5CQH9 |
Ligands and binding sites
- R78 · 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.53 | 0.82 | 21 | R78 |
| 2 | 98 | 0.53 | 0.83 | 20 | R78 |
| 3 | 175 | 0.49 | 0.77 | 32 | empty |
| 4 | 120 | 0.41 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 443 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6MF9 · Crystal structure of CGD4-650 with compound BI2536 · 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 Q5CQH9
- Elsewhere: RCSB PDB 6MF9 · PDBe 6MF9 · UniProt Q5CQH9
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