SMTL ID : 5j7p.1

Macrophage Migration Inhibitory Factor bound to Covalent Inhibitor RDR03785

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

3 x 6H1: 6-{[4-(trifluoromethyl)phenyl]methyl}-2H-1,3-benzodioxol-5-ol(Covalent)

6H1.1: 11 residues within 4Å: Chain A: P.1, M.2, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 Chain C: Y.95, N.97 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain A pi-Stacking: C:Y.95, A:Y.36 Hydrophobic interactions: A:P.1, A:M.2, A:Y.36, A:I.64 Hydrogen bonds: A:P.1, A:I.64 6H1.8: 12 residues within 4Å: Chain A: Y.95, N.97 Chain B: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.1, B:M.2, B:Y.36, B:I.64, B:V.106 Hydrogen bonds: B:P.1, B:I.64 pi-Stacking: B:Y.36, A:Y.95 6H1.13: 12 residues within 4Å: Chain B: 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 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain C pi-Stacking: B:Y.95 Hydrophobic interactions: C:P.1, C:M.2, C:Y.36, C:I.64, C:V.106 Hydrogen bonds: C:P.1, C:I.64

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

SO4.2: 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:D.16 SO4.3: 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 SO4.4: 5 residues within 4Å: Chain A: D.16, G.17, F.18, L.19, S.20 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.16, A:G.17, A:G.17, A:L.19, A:S.20 Water bridges: A:F.18, A:F.18 SO4.5: 2 residues within 4Å: Chain A: A.70, R.73 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.73 SO4.9: 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 SO4.10: 2 residues within 4Å: Chain B: A.70, R.73 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.70 Salt bridges: B:R.73 SO4.14: 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 IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.6: 2 residues within 4Å: Chain A: N.102, A.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.103 IPA.7: 3 residues within 4Å: Chain A: G.65, K.66, Q.71 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.66 Hydrogen bonds: A:K.66 Water bridges: A:I.67

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 3 residues within 4Å: Chain B: G.65, K.66, Q.71 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.66, B:I.67, B:Q.71 GOL.12: 2 residues within 4Å: Chain B: P.15, D.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.16 GOL.15: 3 residues within 4Å: Chain C: G.65, K.66, Q.71 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.66, C:I.67, C:Q.71, C:Q.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cisneros, J.A. et al., Irregularities in enzyme assays: The case of macrophage migration inhibitory factor. Bioorg.Med.Chem.Lett. (2016)

Release Date

2016-05-04

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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