SMTL ID : 3wnr.1

Multiple binding modes of benzyl isothiocyanate inhibitor complexed with Macrophage Migration Inhibitory Factor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-trimer

Ligands

3 x 9BE: N-benzylthioformamide(Covalent)

9BE.1: 8 residues within 4Å: Chain A: P.1, M.2, K.32, Y.36, H.62, I.64, F.113 Chain C: Y.95 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:Y.95, A:Y.36 Hydrophobic interactions: A:I.64, A:I.64 Water bridges: A:I.64 pi-Stacking: A:F.113 9BE.8: 11 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 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.62, B:I.64, B:V.106, B:V.106 Hydrogen bonds: B:H.62 Water bridges: B:I.64 pi-Stacking: A:Y.95 9BE.11: 8 residues within 4Å: Chain B: Y.95 Chain C: P.1, M.2, K.32, Y.36, H.62, I.64, F.113 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.64, C:I.64 Hydrogen bonds: C:Y.36 Water bridges: C:I.64 pi-Stacking: C:F.113

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

SO4.2: 4 residues within 4Å: Chain A: G.68, G.69, A.70, Q.71 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.68, A:G.69, A:A.70, A:Q.71, A:Q.71 SO4.3: 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:I.67 Salt bridges: A:K.66 SO4.4: 2 residues within 4Å: Chain A: A.70, R.73 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.73 SO4.9: 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 SO4.12: 4 residues within 4Å: Chain C: G.68, G.69, A.70, Q.71 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.70, C:Q.71, C:Q.71

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: A.114 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.114 GOL.6: 4 residues within 4Å: Chain A: W.108, T.112, A.114 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.112, A:A.114 GOL.7: 5 residues within 4Å: Chain A: Q.35, Y.36, W.108 Chain C: F.49, D.92 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.92 GOL.13: 4 residues within 4Å: Chain B: F.49 Chain C: Q.35, Y.36, W.108 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.35 Water bridges: B:D.92, B:D.92 GOL.14: 3 residues within 4Å: Chain C: G.65, K.66, Q.71 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.66, C:Q.71, C:Q.71 Water bridges: C:I.67, C:D.100

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

CL.10: 2 residues within 4Å: Chain B: K.32, K.66 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spencer, E.S. et al., Multiple binding modes of isothiocyanates that inhibit macrophage migration inhibitory factor. Eur.J.Med.Chem. (2015)

Release Date

2014-03-05

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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