MolNFT v1 · #145011 · protein
Macrophage migration inhibitory factor in complex with a pyrazole inhibitor (5)
6CBG: “Macrophage migration inhibitory factor in complex with a pyrazole inhibitor (5)”. X-ray diffraction, 2 ligands (EWG, SO4), 4 pockets (best druggability 0.82). MolNFT v1 #145011 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6CBG
- Type
- protein
- Length
- 341 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
- EWG, SO4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 114 | 39% helix, 31% strand | P14174 |
| B | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 113 | 36% helix, 31% strand | P14174 |
Ligands and binding sites
- EWG · 3-(1H-pyrazol-4-yl)benzoic acid · ligand · 2 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 9 copies · chains A, C, 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 | 631 | 0.82 | 0.86 | 63 | empty |
| 2 | 69 | 0.59 | 0.89 | 13 | EWG |
| 3 | 66 | 0.56 | 0.87 | 13 | EWG |
| 4 | 55 | 0.49 | 0.86 | 13 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 1139 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1115 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1101 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6CBG · Macrophage Migration Inhibitory Factor in Complex with a Pyrazole Inhibitor (5) · 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 6CBG · PDBe 6CBG · UniProt P14174
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