MolNFT v1 · #109063 · protein

Macrophage migration inhibitory factor in complex with a biaryltriazole inhibitor (3B-180)

4WR8: “Macrophage migration inhibitory factor in complex with a biaryltriazole inhibitor (3B-180)”. X-ray diffraction, 3 ligands (3TX, NA, SO4), 20 pockets (best druggability 0.84). MolNFT v1 #109063 on GenesisL1: 3D structure, binding…

PDB: 4WR8
Type: protein
Length: 2,052 residues
Chains: 18
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: 3TX, NA, SO4
Pockets: 20 · 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, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12)	protein	114	39% helix, 31% strand	P14174

Ligands and binding sites

3TX · 4-[4-(quinolin-2-yl)-1H-1,2,3-triazol-1-yl]phenol · ligand · 6 copies · chains B, C, F, E, H, I, K, L, O, N, Q, R
NA · Sodium ion · metal · 3 copies · chains F, L
SO4 · Sulfate ion · ion · 53 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	392	0.84	0.92	48	empty
2	1058	0.83	0.83	115	3TX, SO4, NA
3	451	0.82	0.90	49	empty
4	458	0.82	0.89	51	empty
5	419	0.82	0.90	49	empty

Interfaces

38 interfaces between chains.

P–R · 1161 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 1159 Å² buried · 21 hydrogen bonds · protein-protein
D–F · 1155 Å² buried · 20 hydrogen bonds · protein-protein
Q–R · 1152 Å² buried · 17 hydrogen bonds · protein-protein
J–L · 1150 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

4WR8 · Macrophage Migration Inhibitory Factor in complex with a biaryltriazole inhibitor (3b-180) · 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 4WR8 · PDBe 4WR8 · UniProt P14174

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