SMTL ID : 7e4a.1

Crystal structure of MIF bound to compound 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-trimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: G.68, G.69, A.70, Q.71 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: M.101, N.102, N.105 Ligand excluded by PLIP CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: P.1, S.63, I.64 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: P.1, K.32, S.63, I.64 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Ligands: HWL.5 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: 4 residues within 4Å: Chain C: G.68, G.69, A.70, Q.71 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: Y.95 Chain C: P.1, S.63, I.64 Ligands: HWL.13 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain C: M.101, N.102, N.105 Ligand excluded by PLIP

2 x HWL: Flavoxate(Non-covalent)

HWL.5: 7 residues within 4Å: Chain A: F.49, D.92, R.93 Chain B: Q.35, Y.36, W.108 Ligands: CL.8 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.108, A:F.49 pi-Stacking: B:Y.36 Hydrogen bonds: A:R.93 Water bridges: A:S.52 HWL.13: 7 residues within 4Å: Chain B: F.49, Y.95 Chain C: Q.35, Y.36, W.108, F.113 Ligands: CL.11 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Y.36, C:Y.36, C:W.108, C:W.108, C:W.108, C:F.113, C:F.113, C:F.113 Hydrogen bonds: C:Q.35 pi-Stacking: C:Y.36, C:W.108, B:Y.95

1 x NA: SODIUM ION(Non-functional Binders)

NA.14: 3 residues within 4Å: Chain B: G.51 Chain C: S.20, Q.24 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.20, C:Q.24

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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