SMTL ID : 6peg.1

MIF with a allosteric inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: Q.35, Y.36, W.108 Chain B: Y.95 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.36 Water bridges: A:Q.35, B:D.92 ACT.3: 5 residues within 4Å: Chain A: P.1, M.2, S.63, I.64 Chain B: Y.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.1, A:S.63, A:I.64 ACT.10: 8 residues within 4Å: Chain B: P.1, M.2, H.62, S.63, I.64, V.106 Chain C: Y.95, N.97 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:M.2, B:H.62 Hydrogen bonds: B:P.1, B:I.64 ACT.11: 2 residues within 4Å: Chain C: G.65, K.66 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.66 Water bridges: C:I.67

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: G.65, K.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.66 Water bridges: A:G.65, A:Q.71 GOL.9: 7 residues within 4Å: Chain A: Y.95 Chain C: P.1, K.32, Y.36, H.62, S.63, I.64 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.36, C:I.64, C:I.64

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: G.68, G.69, A.70, Q.71 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.69, A:A.70, A:Q.71, A:Q.71 SO4.6: 6 residues within 4Å: Chain A: H.62, Y.99 Chain B: H.62, Y.99 Chain C: H.62, Y.99 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:Y.99, B:Y.99 Salt bridges: C:H.62, B:H.62, A:H.62 SO4.12: 4 residues within 4Å: Chain C: G.68, G.69, A.70, Q.71 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.68, C:G.69, C:A.70, C:Q.71, C:Q.71

1 x 4FQ: 4-amino-5-hydroxy-6-[(E)-(3-{[3-(2-methylpropanoyl)pyrazolo[1,5-a]pyridin-2-yl]methyl}phenyl)diazenyl]naphthalene-1,3-disulfonic acid(Non-covalent)

4FQ.5: 12 residues within 4Å: Chain B: K.32, Q.35, Y.36, I.64, G.65, K.66, A.103, W.108, F.113 Chain C: F.49, Y.95 Ligands: PO4.8 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Q.35, B:Y.36, B:I.64, B:A.103, B:W.108, C:F.49 Hydrogen bonds: B:K.32, B:I.64 Water bridges: B:K.32, B:K.32, B:G.65, B:K.66 Salt bridges: B:K.32, B:K.66 pi-Stacking: B:Y.36, B:W.108, B:W.108, B:W.108, B:F.113

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 4 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.69, B:A.70, B:Q.71, B:Q.71 Water bridges: B:R.73 PO4.8: 6 residues within 4Å: Chain B: K.32, Y.36, I.64, F.113 Chain C: Y.95 Ligands: 4FQ.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Water bridges: B:P.1, B:K.32, B:K.32 Salt bridges: B:K.32 Hydrogen bonds: C:Y.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cirillo, P.F. et al., Inhibition of Macrophage Migration Inhibitory Factor by a Chimera of Two Allosteric Binders. Acs Med.Chem.Lett. (2020)

Release Date

2019-11-27

Peptides

Macrophage migration inhibitory factor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Macrophage migration inhibitory factor

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