Research workbench
Chicago sky blue 6B, a novel inhibitor for macrophage migration inhibitory factor
Analyse Chicago sky blue 6B, a novel inhibitor for macrophage migration inhibitory… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U18
- Type
- protein
- Length
- 342 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage migration inhibitory factor
- EC
- 5.3.2.1, 5.3.3.12
- UniProt
- P14174
- Ligands
- Y0X, NA, SO4
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 114 | 39% helix, 31% strand | P14174 |
Ligands and binding sites
- Y0X · 6,6'-[(3,3'-dimethoxybiphenyl-4,4'-diyl)di(E)diazene-2,1-diyl]bis(4-amino-5-hydroxynaphthalene-1,3-disulfonic acid) · ligand · chains A, C
- NA · Sodium ion · metal · 4 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- GOL · Glycerol · additive · 9 copies · chains A, C, B
- IPA · Isopropyl alcohol · additive · 4 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.83 | 0.90 | 49 | NA |
| 2 | 63 | 0.53 | 0.86 | 13 | IPA, GOL |
| 3 | 51 | 0.51 | 0.87 | 13 | IPA, GOL |
| 4 | 157 | 0.42 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1151 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1144 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1142 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3U18 · Chicago Sky Blue 6B, A Novel Inhibitor for Macrophage Migration Inhibitory Factor · 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 P14174
- Elsewhere: RCSB PDB 3U18 · PDBe 3U18 · UniProt P14174
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