SMTL ID : 2ooh.1

Crystal Structure of MIF bound to a Novel Inhibitor, OXIM-11

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

8 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 SO4.2: 1 residues within 4Å: Chain A: R.73 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Water bridges: C:S.111, C:S.111, A:R.73, A:R.73 Salt bridges: A:R.73 SO4.3: 2 residues within 4Å: Chain A: P.15, D.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.16 Water bridges: A:G.17 SO4.4: 2 residues within 4Å: Chain A: A.70, R.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.70 Salt bridges: A:R.73 SO4.5: 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: 2 interactions with chain B, 3 interactions with chain A, 1 interactions with chain C Water bridges: B:Y.99, A:Y.99 Salt bridges: B:H.62, A:H.62, C:H.62 Hydrogen bonds: A:Y.99 SO4.6: 4 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.68, B:G.69, B:A.70, B:Q.71, B:Q.71 SO4.7: 5 residues within 4Å: Chain B: D.16, G.17, F.18, L.19, S.20 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.16, B:G.17, B:G.17, B:L.19, B:S.20 Water bridges: B:F.18, B:F.18 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

2 x OX3: 4-HYDROXYBENZALDEHYDE O-(CYCLOHEXYLCARBONYL)OXIME(Non-covalent)

OX3.8: 13 residues within 4Å: Chain B: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 Chain C: Y.95, N.97 Ligands: GOL.11 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.36, B:Y.36, B:H.62, B:I.64, B:M.101, B:V.106, B:F.113, C:Y.95, C:Y.95 Hydrogen bonds: B:I.64 OX3.10: 13 residues within 4Å: Chain A: Y.95, N.97 Chain C: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 Ligands: GOL.12 13 PLIP interactions: 2 interactions with chain A, 11 interactions with chain C Hydrophobic interactions: A:Y.95, A:Y.95, C:M.2, C:K.32, C:H.62, C:I.64, C:I.64, C:M.101, C:V.106, C:F.113 Hydrogen bonds: C:I.64 Water bridges: C:K.32 Salt bridges: C:K.32

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 9 residues within 4Å: Chain B: P.1, M.2, H.62, S.63, M.101, V.106 Chain C: Y.95, N.97 Ligands: OX3.8 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Y.95, C:N.97, C:N.97, B:M.2, B:I.64 GOL.12: 8 residues within 4Å: Chain A: N.97 Chain C: P.1, M.2, H.62, S.63, I.64, M.101 Ligands: OX3.10 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.97, C:I.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crichlow, G.V. et al., Alternative chemical modifications reverse the binding orientation of a pharmacophore scaffold in the active site of macrophage migration inhibitory factor. J.Biol.Chem. (2007)

Release Date

2007-06-05

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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