MolNFT v1 · #143529 · protein
Macrophage migration inhibitory factor in complex with a naphthyridinone inhibitor (4B)
6B2C: “Macrophage migration inhibitory factor in complex with a naphthyridinone inhibitor (4B)”. X-ray diffraction, 2 ligands (C9Y, SO4), 5 pockets (best druggability 0.84). MolNFT v1 #143529 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6B2C
- 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
- C9Y, SO4
- Pockets
- 5 · best druggability 0.84
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
- C9Y · {2-[1-(3-fluoro-4-hydroxyphenyl)-1H-1,2,3-triazol-4-yl]-8-oxo-1,7-naphthyridin-7(8H)-yl}acetic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion · chains A
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 | 470 | 0.84 | 0.90 | 48 | empty |
| 2 | 72 | 0.54 | 0.86 | 13 | C9Y |
| 3 | 72 | 0.53 | 0.85 | 13 | empty |
| 4 | 79 | 0.51 | 0.84 | 16 | empty |
| 5 | 138 | 0.39 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1200 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1156 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1138 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6B2C · Macrophage Migration Inhibitory Factor in Complex with a Naphthyridi Inhibitor (4b) · 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 6B2C · PDBe 6B2C · UniProt P14174
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