MolNFT v1 · #117523 · protein
Crystal structure of human WDR5 in complex with compound 9O
5EAM · Wd repeat-containing protein 5: “Crystal structure of human WDR5 in complex with compound 9O”. X-ray diffraction, 3 ligands (5MN, UNX, SO4), 5 pockets (best druggability 0.82). MolNFT v1 #117523 on GenesisL1: 3D structure, binding…
- PDB
- 5EAM
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5
- UniProt
- P61964
- Ligands
- 5MN, UNX, SO4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Wd repeat-containing protein 5 | protein | 304 | 0% helix, 52% strand | P61964 |
Ligands and binding sites
- 5MN · ~{N}-[5-(1~{H}-indol-5-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methyl-benzamide · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 25 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.82 | 0.87 | 51 | SO4, BTB, EDO |
| 2 | 678 | 0.76 | 0.82 | 65 | 5MN, EDO, UNX |
| 3 | 218 | 0.59 | 0.80 | 32 | 5MN, UNX |
| 4 | 223 | 0.57 | 0.79 | 29 | empty |
| 5 | 76 | 0.36 | 0.77 | 18 | UNX |
Interfaces
1 interface between chains.
- A–B · 494 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5EAM · Crystal structure of human WDR5 in complex with compound 9o · 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 5EAM · PDBe 5EAM · UniProt P61964
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.