SMTL ID : 3wns.1

Allyl isothiocyanate inhibitor complexed with Macrophage Migration Inhibitory Factor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-trimer

Ligands

3 x 9AI: N-prop-2-en-1-ylthioformamide(Covalent)

9AI.1: 7 residues within 4Å: Chain A: P.1, M.2, Y.36, H.62, V.106 Chain C: Y.95, N.97 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.106, C:Y.95 Hydrogen bonds: A:H.62 Water bridges: A:I.64 9AI.5: 7 residues within 4Å: Chain A: Y.95, N.97 Chain B: P.1, M.2, Y.36, H.62, V.106 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.106 Hydrogen bonds: B:H.62 Water bridges: B:I.64 9AI.10: 6 residues within 4Å: Chain B: Y.95, N.97 Chain C: P.1, M.2, H.62, V.106 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:V.106, B:Y.95, B:Y.95 Hydrogen bonds: C:H.62 Water bridges: C:I.64

6 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 SO4.6: 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 SO4.7: 5 residues within 4Å: Chain B: D.16, G.17, F.18, L.19, S.20 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.17, B:F.18, B:L.19, B:S.20, B:S.20 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:G.65, B:Q.71, B:D.100 SO4.11: 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 SO4.12: 2 residues within 4Å: Chain C: P.15, D.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.16

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

IPA.3: 3 residues within 4Å: Chain A: G.17, E.21, Q.24 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.21 Hydrogen bonds: A:Q.24

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

CL.4: 3 residues within 4Å: Chain A: M.101, N.102, N.105 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: D.92 Chain B: Q.35, Y.36, W.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.92 GOL.13: 5 residues within 4Å: Chain A: L.19, S.20 Chain C: A.48, G.51, S.53 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.20 Water bridges: C:S.53, C:S.53 GOL.14: 1 residues within 4Å: Chain C: R.86 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.86

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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