SMTL ID : 6cbh.1

Macrophage Migration Inhibitory Factor in Complex with a Pyrazole Inhibitor (8m)

Coordinates

PDB Format Compare

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 SO4.2: 6 residues within 4Å: Chain A: H.62, Y.99 Chain B: H.62, Y.99 Chain C: H.62, Y.99 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B Water bridges: A:N.97, C:Y.99, B:H.62 Salt bridges: A:H.62, B:H.62 Hydrogen bonds: C:Y.99 SO4.6: 1 residues within 4Å: Chain B: R.86 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.86, B:R.86 Salt bridges: B:R.86 SO4.7: 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:A.70, B:Q.71, B:Q.71 Water bridges: B:G.69, B:G.69 SO4.8: 1 residues within 4Å: Chain C: R.86 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.86 SO4.10: 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:A.70, C:Q.71, C:Q.71 Water bridges: C:G.69, C:G.69

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 3 residues within 4Å: Chain A: Q.35, Y.36, W.108 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.36 Water bridges: C:D.92 IPA.11: 4 residues within 4Å: Chain B: Y.95 Chain C: Q.35, Y.36, W.108 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.36, C:Y.36, C:W.108, C:W.108

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: N.97 Chain B: P.1, M.2, H.62, S.63, I.64, M.101, V.106 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.62, B:I.64, A:N.97, A:N.97 GOL.5: 9 residues within 4Å: Chain A: P.1, M.2, H.62, S.63, I.64, M.101, V.106 Chain C: Y.95, N.97 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.97, A:P.1

1 x EWJ: 5-(3-fluoro-1H-pyrazol-4-yl)-2-[(naphthalen-2-yl)oxy]benzoic acid(Non-covalent)

EWJ.9: 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, F.113 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:Y.95, C:I.64, C:I.64, C:V.106, C:F.113, C:F.113 Hydrogen bonds: B:N.97, B:N.97, C:P.1, C:I.64 pi-Stacking: B:Y.95, C:F.113 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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