SMTL ID : 7e45.1

Crystal structure of compound 7 bound to MIF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-trimer

Ligands

13 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: P.1, K.32, S.63, I.64 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: G.68, G.69, A.70, Q.71 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: M.101, N.102, N.105 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: S.60, N.97, Y.99 Chain B: H.62 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: P.1, K.32, S.63, I.64 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: M.101, N.102, N.105 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: G.65, K.66 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: P.15, G.17, F.18, L.19 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: E.21, Q.24, Q.25 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain C: P.1, K.32, S.63, I.64 Ligands: HWO.11 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: H.62 Chain C: S.60, N.97, Y.99 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: M.101, N.102, N.105 Ligand excluded by PLIP

1 x HWO: (2R)-7-[(2R,3R,4R,5S,6S)-6-(hydroxymethyl)-3-[(2R,3R,4R,5R,6S)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-(4-methoxy-3-oxidanyl-phenyl)-5-oxidanyl-2,3-dihydrochromen-4-one(Non-covalent)

HWO.11: 7 residues within 4Å: Chain B: D.92, Y.95 Chain C: Y.36, I.64, W.108, F.113 Ligands: CL.12 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:D.92, B:D.92 Water bridges: B:D.92, B:Y.95, C:N.109 Hydrophobic interactions: C:Y.36, C:I.64, C:W.108, C:F.113 pi-Stacking: C:Y.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, L. et al., Identification and Structure-Activity Relationships of Dietary Flavonoids as Human Macrophage Migration Inhibitory Factor (MIF) Inhibitors. J.Agric.Food Chem. (2021)

Release Date

2023-02-15

Peptides

Macrophage migration inhibitory factor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Macrophage migration inhibitory factor

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