SMTL ID : 3ijj.1

Ternary Complex of Macrophage Migration Inhibitory Factor (MIF) Bound Both to 4-hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-stereoisomer)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-trimer

Ligands

3 x EN1: (2E)-2-hydroxy-3-(4-hydroxyphenyl)prop-2-enoic acid(Non-covalent)

EN1.1: 12 residues within 4Å: Chain A: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106 Chain C: Y.95, N.97 Ligands: ENO.2 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:I.64, A:V.106, C:Y.95 Hydrogen bonds: A:I.64, C:N.97 Water bridges: A:K.32, A:K.32 Salt bridges: A:K.32 pi-Stacking: C:Y.95 EN1.6: 13 residues within 4Å: Chain A: Y.95, N.97 Chain B: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 Ligands: ENO.7 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.64, B:V.106, B:F.113, A:Y.95 Hydrogen bonds: B:I.64, A:N.97 Salt bridges: B:K.32 pi-Stacking: A:Y.95 EN1.10: 12 residues within 4Å: Chain B: Y.95, N.97 Chain C: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106 Ligands: ENO.11 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:H.62, C:I.64, C:V.106, C:V.106, B:Y.95 Hydrogen bonds: C:P.1, C:I.64, B:N.97 Salt bridges: C:K.32 pi-Stacking: B:Y.95

3 x ENO: 3-(4-HYDROXY-PHENYL)PYRUVIC ACID(Covalent)(Non-covalent)

ENO.2: 13 residues within 4Å: Chain A: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 Chain C: Y.95, N.97 Ligands: EN1.1 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:P.1, A:P.1, A:M.2, A:H.62, A:I.64, A:V.106 Hydrogen bonds: A:P.1, A:I.64, C:N.97 Water bridges: A:K.32, A:K.32 Salt bridges: A:K.32 pi-Stacking: C:Y.95 ENO.7: 12 residues within 4Å: Chain A: Y.95, N.97 Chain B: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, F.113 Ligands: EN1.6 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.1, B:P.1, B:M.2, B:H.62, B:I.64 Hydrogen bonds: B:P.1, B:I.64, A:N.97, A:N.97 Water bridges: B:K.32 Salt bridges: B:K.32 pi-Stacking: A:Y.95 ENO.11: 12 residues within 4Å: Chain B: Y.95, N.97 Chain C: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, F.113 Ligands: EN1.10 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:M.2, C:H.62, C:I.64, C:M.101 Hydrogen bonds: C:P.1, C:I.64, B:Y.95, B:N.97 Salt bridges: C:K.32 pi-Stacking: B:Y.95

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

CL.3: 4 residues within 4Å: Chain A: G.68, G.69, A.70, Q.71 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: M.101, N.102, N.105 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: A.70, R.73 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: M.101, N.102, N.105 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain C: G.68, G.69, A.70, Q.71 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: M.101, N.102, N.105 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: A.70, R.73 Ligand excluded by PLIP

1 x AVR: (2R)-2-amino-1-[2-(1-methylethyl)pyrazolo[1,5-a]pyridin-3-yl]propan-1-one(Non-covalent)

AVR.12: 5 residues within 4Å: Chain B: Y.95 Chain C: Q.35, Y.36, W.108, F.113 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Q.35, C:W.108 pi-Stacking: C:Y.36, C:Y.36, C:W.108, C:W.108, C:W.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cho, Y. et al., Allosteric inhibition of macrophage migration inhibitory factor revealed by ibudilast. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-06-16

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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