SMTL ID : 9bnq.1

N-(4-(isothiocyanatomethyl)phenyl)methanesulfonamide complexed with Macrophage Migration Inhibitory Factor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.09 Å

Oligo State

homo-trimer

Ligands

3 x 01: N-{[4-(methanesulfonamido)phenyl]methyl}methanethioamide

01.1: 12 residues within 4Å: Chain A: P.1, M.2, K.32, Y.36, I.37, H.62, S.63, I.64, A.103, V.106, F.113 Chain C: Y.95 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.36, A:I.64, A:I.64 Hydrogen bonds: A:K.32, A:Y.36, A:I.64, C:Y.95 pi-Stacking: A:F.113 01.5: 12 residues within 4Å: Chain A: Y.95 Chain B: P.1, M.2, K.32, Y.36, I.37, H.62, S.63, I.64, V.106, F.113 Ligands: IPA.4 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.64 Hydrogen bonds: B:K.32, B:Y.36, A:Y.95 pi-Stacking: B:Y.36, B:F.113 01.8: 11 residues within 4Å: Chain B: Y.95 Chain C: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, V.106, F.113 Ligands: IPA.7 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.64 Hydrogen bonds: C:K.32, C:Y.36, B:Y.95 pi-Stacking: C:Y.36, C:F.113

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

SO4.2: 5 residues within 4Å: Chain A: D.16, G.17, F.18, L.19, S.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.17, A:G.17, A:L.19, A:S.20 SO4.3: 4 residues within 4Å: Chain A: G.65, K.66, I.67, Q.71 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.66 Water bridges: A:I.67, A:D.100 Salt bridges: A:K.66 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 SO4.9: 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 SO4.10: 4 residues within 4Å: Chain C: P.15, E.85, R.86, R.88 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.85 Water bridges: C:R.86, C:R.86, C:R.88, C:R.88 Salt bridges: C:R.86

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

IPA.4: 8 residues within 4Å: Chain A: F.49, D.92, Y.95 Chain B: Q.35, Y.36, W.108, F.113 Ligands: 01.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.36, B:W.108, B:F.113, A:F.49 Water bridges: B:Q.35 IPA.7: 7 residues within 4Å: Chain B: F.49, Y.95 Chain C: Q.35, Y.36, W.108, F.113 Ligands: 01.8 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.36, C:F.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tyndall, J. et al., Covalent isothiocyanate inhibitors of macrophage migration inhibitory factor as potential colorectal cancer treatments. Chemmedchem (2024)

Release Date

2024-07-24

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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