SMTL ID : 6b1k.1

Macrophage Migration Inhibitory Factor in Complex with a Naphthyridinone Inhibitor (3a)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

homo-trimer

Ligands

3 x C9G: 2-[1-(4-hydroxyphenyl)-1H-1,2,3-triazol-4-yl]-7-methyl-1,7-naphthyridin-8(7H)-one(Non-covalent)

C9G.1: 13 residues within 4Å: Chain A: P.1, M.2, K.32, P.33, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 Chain C: Y.95, N.97 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:M.2, A:P.33, A:Y.36, A:H.62, A:I.64, A:V.106, A:V.106, A:F.113 Hydrogen bonds: A:K.32, A:I.64, C:N.97, C:N.97 pi-Stacking: C:Y.95 C9G.4: 13 residues within 4Å: Chain A: Y.95, N.97 Chain B: P.1, M.2, K.32, P.33, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:M.2, B:P.33, B:Y.36, B:H.62, B:I.64, B:V.106, B:F.113 Hydrogen bonds: B:P.1, B:K.32, B:I.64, A:N.97, A:N.97 pi-Stacking: A:Y.95 C9G.6: 12 residues within 4Å: Chain B: Y.95, N.97 Chain C: P.1, M.2, K.32, P.33, Y.36, H.62, S.63, I.64, M.101, V.106 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:M.2, C:P.33, C:Y.36, C:H.62, C:I.64, C:V.106 Hydrogen bonds: C:P.1, C:K.32, C:I.64, B:N.97, B:N.97 pi-Stacking: B:Y.95

4 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 SO4.5: 2 residues within 4Å: Chain B: G.68, G.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.69 Water bridges: B:A.70 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: 5 residues within 4Å: Chain C: D.16, G.17, F.18, L.19, S.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.17, C:F.18, C:L.19, C:S.20

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: F.49, D.92, R.93 Chain B: Q.35, Y.36, W.108 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.92 Water bridges: A:D.92, A:D.92, B:Y.36, B:Y.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dawson, T.K. et al., Adding a Hydrogen Bond May Not Help: Naphthyridinone vs Quinoline Inhibitors of Macrophage Migration Inhibitory Factor. ACS Med Chem Lett (2017)

Release Date

2018-01-03

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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