SMTL ID : 3wnt.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-trimer

Ligands

3 x 9BE: N-benzylthioformamide(Covalent)

9BE.1: 11 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 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:H.62, A:I.64, A:V.106, A:V.106 Hydrogen bonds: A:P.1 Water bridges: A:I.64 pi-Stacking: C:Y.95 9BE.4: 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 6 PLIP interactions: 5 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:P.1 pi-Stacking: A:Y.95 9BE.6: 9 residues within 4Å: Chain B: Y.95, N.97 Chain C: P.1, M.2, H.62, S.63, I.64, M.101, V.106 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:H.62, C:I.64, C:M.101, C:V.106, C:V.106 Hydrogen bonds: C:H.62 pi-Stacking: B:Y.95

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

SO4.2: 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 SO4.3: 1 residues within 4Å: Chain A: R.86 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.86 SO4.5: 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:I.67 SO4.7: 4 residues within 4Å: Chain C: G.68, G.69, A.70, Q.71 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.69, C:A.70, C:Q.71, C:Q.71 SO4.8: 1 residues within 4Å: Chain C: R.86 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.86 Salt bridges: C:R.86

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

IPA.9: 1 residues within 4Å: Chain C: G.50 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.35

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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