SMTL ID : 3u18.1

Chicago Sky Blue 6B, A Novel Inhibitor for Macrophage Migration Inhibitory Factor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

1 x Y0X: 6,6'-[(3,3'-dimethoxybiphenyl-4,4'-diyl)di(E)diazene-2,1-diyl]bis(4-amino-5-hydroxynaphthalene-1,3-disulfonic acid)(Non-covalent)

Y0X.1: 14 residues within 4Å: Chain A: K.32, Y.36, I.64, G.65, K.66, A.103, W.108, N.109, N.110, S.111, T.112, F.113 Chain C: P.91 Ligands: IPA.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.64, A:A.103 Hydrogen bonds: A:K.32, A:K.66, A:N.109, A:N.110 Water bridges: A:G.65, A:G.65, A:K.66, A:K.66 Salt bridges: A:K.32, A:K.66 pi-Stacking: A:W.108, A:F.113

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

IPA.2: 6 residues within 4Å: Chain A: K.32, Y.36, I.64, F.113 Ligands: Y0X.1, GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.36, A:F.113, A:F.113 Hydrogen bonds: A:K.32, A:I.64 IPA.17: 2 residues within 4Å: Chain B: K.32, I.64 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.64 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 IPA.23: 3 residues within 4Å: Chain C: Q.35, Y.36, W.108 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Y.36, C:W.108 Water bridges: B:D.92, B:D.92

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.11, V.14, P.15, D.16, G.17, F.18, L.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.11, A:V.14, A:G.17, A:F.18, A:L.19 GOL.4: 10 residues within 4Å: Chain A: P.1, M.2, H.62, S.63, I.64, M.101, V.106 Chain C: Y.95, N.97 Ligands: IPA.2 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:P.1, A:I.64, C:N.97, C:N.97 GOL.8: 4 residues within 4Å: Chain A: G.51, S.52, S.53 Chain B: L.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.53, A:S.53 GOL.10: 3 residues within 4Å: Chain B: G.65, K.66, Q.71 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.66, B:Q.71, B:Q.71 Water bridges: B:I.67 GOL.14: 8 residues within 4Å: Chain A: Y.95, N.97 Chain B: P.1, M.2, H.62, S.63, I.64, V.106 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.62, B:I.64, A:N.97, A:N.97 GOL.16: 7 residues within 4Å: Chain A: L.46 Chain B: R.11, V.14, P.15, G.17, F.18, L.19 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.11, B:R.11, B:V.14, B:G.17, B:L.19 Water bridges: B:D.16 GOL.19: 8 residues within 4Å: Chain B: Y.95, N.97 Chain C: P.1, M.2, H.62, S.63, I.64, V.106 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:P.1, C:H.62, C:I.64, B:N.97, B:N.97 Water bridges: C:S.63 GOL.21: 6 residues within 4Å: Chain C: P.15, D.16, G.17, F.18, L.19, S.20 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.17, C:F.18, C:L.19, C:S.20, C:S.20 GOL.22: 4 residues within 4Å: Chain C: G.65, K.66, I.67, Q.71 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.66, C:K.66, C:I.67, C:I.67, C:Q.71

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 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 EDO.11: 6 residues within 4Å: Chain B: N.8, P.10, S.53, E.54, P.55 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.53 EDO.15: 6 residues within 4Å: Chain B: V.9, P.10, S.13, L.87, R.88 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.13, B:L.87

4 x NA: SODIUM ION(Non-functional Binders)

NA.6: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.53, A:S.53 NA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.9: 4 residues within 4Å: Chain A: S.60, N.97, Y.99 Chain B: H.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.97 NA.13: 4 residues within 4Å: Chain B: S.60, N.97, Y.99 Chain C: H.62 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.99, C:H.62 Water bridges: B:N.97

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

SO4.12: 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 SO4.20: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, F. et al., A Novel Allosteric Inhibitor of Macrophage Migration Inhibitory Factor (MIF). J.Biol.Chem. (2012)

Release Date

2012-07-18

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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