SMTL ID : 7e47.1

Crystal structure of compound 6 bound to MIF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-trimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: M.101, N.102, N.105 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: P.1, S.63, I.64 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain B: M.101, N.102, N.105 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: P.1, S.63, I.64 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain C: M.101, N.102, N.105 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain C: P.1, K.32, S.63, I.64 Ligands: HWR.8 Ligand excluded by PLIP

1 x HWR: (2S,3R,4R,5R,6R)-2-[(2S,3R,4S,5R,6S)-6-(hydroxymethyl)-2-[[(2R,4R)-2-(4-hydroxyphenyl)-4,5-bis(oxidanyl)-3,4-dihydro-2H-chromen-7-yl]oxy]-4,5-bis(oxidanyl)oxan-3-yl]oxy-6-methyl-oxane-3,4,5-triol(Non-covalent)

HWR.8: 16 residues within 4Å: Chain B: Y.95, N.97 Chain C: P.1, M.2, K.32, P.33, Y.36, I.37, H.62, S.63, I.64, M.101, V.106, W.108, F.113 Ligands: CL.7 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Y.36, C:Y.36, C:H.62, C:I.64, C:V.106, C:F.113 Hydrogen bonds: C:K.32, C:P.33, B:N.97 Water bridges: C:K.32, C:F.113 Salt bridges: C:K.32 pi-Cation interactions: C:K.32 pi-Stacking: B:Y.95

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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