SMTL ID : 5hvt.1

Crystal Structure of Macrophage Migration Inhibitory Factor (MIF) with a Potent Inhibitor (NVS-2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 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 SO4.3: 6 residues within 4Å: Chain A: H.62, Y.99 Chain B: H.62, Y.99 Chain C: H.62, Y.99 6 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 2 interactions with chain C Water bridges: A:Y.99, B:Y.99, C:H.62 Hydrogen bonds: B:Y.99 Salt bridges: B:H.62, C:H.62 SO4.7: 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: 1 residues within 4Å: Chain B: S.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.53 SO4.10: 2 residues within 4Å: Chain B: P.15, D.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.16 SO4.13: 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

3 x NVS: 7-hydroxy-3-(4-methoxyphenyl)-3,4-dihydro-2H-1,3-benzoxazin-2-one(Non-covalent)

NVS.2: 12 residues within 4Å: Chain A: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 Chain B: Y.95, N.97 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.32, A:Y.36, A:Y.36, A:H.62, A:I.64, A:V.106 Hydrogen bonds: A:P.1, A:I.64, B:N.97 pi-Stacking: A:F.113, B:Y.95 NVS.8: 13 residues within 4Å: Chain B: 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 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.36, B:V.106, B:F.113, B:F.113 Hydrogen bonds: B:I.64, C:N.97 pi-Cation interactions: B:K.32 pi-Stacking: C:Y.95 NVS.14: 13 residues within 4Å: Chain A: 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, F.113 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:N.97, C:I.64 pi-Stacking: A:Y.95 Hydrophobic interactions: C:K.32, C:Y.36, C:H.62, C:V.106, C:F.113, C:F.113

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: Q.35, Y.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.35 GOL.5: 3 residues within 4Å: Chain A: G.65, K.66, Q.71 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.66, A:Q.71, A:Q.71 Water bridges: A:K.32, A:I.67, A:I.67 GOL.11: 5 residues within 4Å: Chain B: D.16, G.17, F.18, L.19, S.20 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.16, B:D.16, B:G.17, B:L.19, B:S.20, B:S.20 Water bridges: B:F.18, B:F.18

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

IPA.6: 2 residues within 4Å: Chain A: A.70, R.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.73, A:R.73 IPA.12: 2 residues within 4Å: Chain B: N.102, A.103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.103 Water bridges: B:M.101 IPA.15: 6 residues within 4Å: Chain C: P.15, D.16, G.17, F.18, L.19, S.20 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.19, C:L.19 Hydrogen bonds: C:G.17, C:F.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cisneros, J.A. et al., A Fluorescence Polarization Assay for Binding to Macrophage Migration Inhibitory Factor and Crystal Structures for Complexes of Two Potent Inhibitors. J.Am.Chem.Soc. (2016)

Release Date

2016-06-29

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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