SMTL ID : 6cbg.1

Macrophage Migration Inhibitory Factor in Complex with a Pyrazole Inhibitor (5)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 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 SO4.7: 4 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.69, B:A.70, B:Q.71, B:Q.71 SO4.8: 2 residues within 4Å: Chain B: G.65, K.66 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.66 Water bridges: B:I.67, B:D.100 Salt bridges: B:K.66 SO4.11: 3 residues within 4Å: Chain C: G.65, K.66 Ligands: GOL.16 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.66 Water bridges: C:I.67 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 SO4.13: 5 residues within 4Å: Chain C: D.16, G.17, F.18, L.19, S.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.17, C:F.18, C:L.19, C:S.20

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: P.1, M.2, H.62, S.63, I.64, V.106 Chain C: Y.95, N.97 Ligands: GOL.3 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:P.1, A:P.1, A:I.64, C:N.97, C:N.97 GOL.3: 7 residues within 4Å: Chain A: P.1, K.32, Y.36, I.64, F.113 Chain C: Y.95 Ligands: GOL.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:P.1, A:I.64, C:Y.95 Water bridges: A:K.32 GOL.4: 3 residues within 4Å: Chain A: K.32, I.64, K.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.32, A:K.32 GOL.5: 2 residues within 4Å: Chain A: D.92 Chain B: W.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.92 GOL.6: 7 residues within 4Å: Chain A: L.46 Chain B: V.14, P.15, D.16, G.17, F.18, L.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.14, B:G.17, B:F.18, B:L.19 GOL.10: 3 residues within 4Å: Chain B: K.32, I.64 Ligands: EWG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.32 GOL.15: 4 residues within 4Å: Chain C: K.32, I.64 Ligands: EWG.14, GOL.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.32 GOL.16: 4 residues within 4Å: Chain C: I.64, G.65 Ligands: SO4.11, GOL.15 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.65 GOL.17: 4 residues within 4Å: Chain B: D.92 Chain C: Q.35, Y.36, W.108 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.35, C:Y.36, B:D.92, B:D.92

2 x EWG: 3-(1H-pyrazol-4-yl)benzoic acid(Non-covalent)

EWG.9: 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: GOL.10 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Y.95, A:Y.95, B:I.64, B:V.106, B:F.113 Hydrogen bonds: A:N.97, A:N.97, B:P.1, B:S.63, B:I.64 Salt bridges: B:K.32 EWG.14: 13 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, F.113 Ligands: GOL.15 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:Y.36, C:I.64, C:V.106, C:F.113, B:Y.95, B:Y.95 Hydrogen bonds: C:I.64, B:N.97, B:N.97 Salt bridges: C:K.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trivedi-Parmar, V. et al., Optimization of Pyrazoles as Phenol Surrogates to Yield Potent Inhibitors of Macrophage Migration Inhibitory Factor. ChemMedChem (2018)

Release Date

2018-04-04

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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