SMTL ID : 4osf.1

4-(2-isothiocyanatoethyl)phenol inhibitor complexed with Macrophage Migration Inhibitory Factor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-trimer

Ligands

3 x 4MT: N-[2-(4-hydroxyphenyl)ethyl]thioformamide(Covalent)

4MT.1: 12 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 Ligands: SO4.4 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:I.64, A:V.106 Hydrogen bonds: A:P.1, C:N.97, C:N.97 Water bridges: A:I.64 pi-Stacking: C:Y.95 4MT.10: 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: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.97, A:N.97, B:P.1 pi-Stacking: A:Y.95 Hydrophobic interactions: B:I.64, B:V.106 4MT.13: 11 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 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:N.97, B:N.97, C:P.1 pi-Stacking: B:Y.95 Hydrophobic interactions: C:I.64, C:V.106

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

SO4.2: 3 residues within 4Å: Chain A: P.15, D.16 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.16, A:D.16 Water bridges: A:G.17 SO4.3: 6 residues within 4Å: Chain A: H.62, Y.99 Chain B: H.62, Y.99 Chain C: H.62, Y.99 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Water bridges: A:Y.99, C:Y.99 Salt bridges: A:H.62, C:H.62, B:H.62 SO4.4: 4 residues within 4Å: Chain A: K.32, Y.36, F.113 Ligands: 4MT.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.32 SO4.5: 1 residues within 4Å: Chain A: R.73 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.73 Water bridges: B:S.111, B:S.111, B:T.112 SO4.6: 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: 2 residues within 4Å: Chain A: A.70, R.73 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.70, A:R.73 Salt bridges: A:R.73 SO4.8: 3 residues within 4Å: Chain A: P.15, R.86 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.86 SO4.11: 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 SO4.14: 5 residues within 4Å: Chain C: D.16, G.17, F.18, L.19, S.20 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.16, C:G.17, C:G.17, C:F.18, C:L.19, C:S.20 SO4.15: 2 residues within 4Å: Chain C: A.70, R.73 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.73 SO4.16: 2 residues within 4Å: Chain C: G.65, K.66 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.66 Water bridges: C:I.67, C:D.100 SO4.17: 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

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

CL.9: 2 residues within 4Å: Chain A: G.65, K.66 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: G.65, K.66 Ligand excluded by PLIP

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

IPA.18: 3 residues within 4Å: Chain C: K.32, I.64, F.113 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.64, C:F.113

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

2014-03-12

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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