Research workbench
Crystal structure of human wd repeat domain 5 in complex with 2- chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5- NITROPHENYL]BENZAMIDE
Analyse Crystal structure of human wd repeat domain 5 in complex with 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IA9
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5
- UniProt
- P61964
- Ligands
- IA9, UNX
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 305 | 0% helix, 51% strand | P61964 |
Ligands and binding sites
- IA9 · 2-chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide · ligand · chains A
- UNX · Unknown atom or ion · ion · 24 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.70 | 0.81 | 34 | UNX |
| 2 | 52 | 0.60 | 0.92 | 18 | empty |
| 3 | 232 | 0.60 | 0.80 | 34 | IA9, UNX |
Compared structures
- 4IA9 · Crystal structure of human WD REPEAT DOMAIN 5 in complex with… · 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 P61964
- Elsewhere: RCSB PDB 4IA9 · PDBe 4IA9 · UniProt P61964
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