SMTL ID : 1gcz.1

MACROPHAGE MIGRATION INHIBITORY FACTOR (MIF) COMPLEXED WITH INHIBITOR.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

10 x SO4: SULFATE ION(Non-functional Binders)(Non-covalent)

SO4.1: 3 residues within 4Å: Chain A: E.116, H.117, H.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.116, A:H.118 Water bridges: A:H.117 Salt bridges: A:H.117 SO4.2: 3 residues within 4Å: Chain A: H.118 Chain C: A.70, R.73 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:H.118 Salt bridges: A:H.118, C:R.73 SO4.3: 3 residues within 4Å: Chain C: E.116, H.117, H.118 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.118 Salt bridges: C:H.117 SO4.4: 3 residues within 4Å: Chain B: A.70, R.73 Chain C: H.118 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.73 Hydrogen bonds: C:H.118 SO4.5: 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 SO4.6: 4 residues within 4Å: Chain C: G.68, G.69, A.70, Q.71 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.68, C:G.69, C:A.70, C:Q.71, C:Q.71 SO4.7: 2 residues within 4Å: Chain C: G.65, K.66 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.66 Water bridges: C:I.67 SO4.8: 2 residues within 4Å: Chain A: G.65, K.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.66 Water bridges: A:I.67, A:I.67 SO4.9: 2 residues within 4Å: Chain A: E.85, R.86 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.86 SO4.10: 1 residues within 4Å: Chain A: G.50 No protein-ligand interaction detected (PLIP)

3 x CIT: CITRIC ACID(Non-covalent)(Non-functional Binders)

CIT.11: 12 residues within 4Å: Chain A: N.6, L.58, C.59, S.60, N.97, Y.99 Chain B: M.2, I.4, H.40, H.62 Ligands: CIT.12, CIT.13 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.4, A:L.58 Water bridges: B:S.60 Salt bridges: B:H.40, B:H.62 Hydrogen bonds: A:N.6, A:S.60, A:N.97 CIT.12: 13 residues within 4Å: Chain B: I.4, N.6, L.58, C.59, S.60, N.97, Y.99 Chain C: M.2, I.4, H.40, H.62 Ligands: CIT.11, CIT.13 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.58, C:I.4 Hydrogen bonds: B:N.6, B:S.60, B:N.97, B:Y.99 Water bridges: C:S.60, C:S.60 Salt bridges: C:H.40, C:H.62 CIT.13: 13 residues within 4Å: Chain A: M.2, I.4, H.40, H.62 Chain C: I.4, N.6, L.58, C.59, S.60, N.97, Y.99 Ligands: CIT.11, CIT.12 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.58, A:I.4 Hydrogen bonds: C:N.6, C:S.60, C:N.97 Water bridges: A:S.60 Salt bridges: A:H.40, A:H.62

3 x YZ9: 7-HYDROXY-2-OXO-CHROMENE-3-CARBOXYLIC ACID ETHYL ESTER(Non-functional Binders)(Non-covalent)

YZ9.14: 10 residues within 4Å: Chain A: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, V.106 Chain C: Y.95, N.97 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:H.62, A:I.64, A:V.106 Hydrogen bonds: A:I.64, C:N.97 Salt bridges: A:K.32, A:K.32 pi-Stacking: C:Y.95 YZ9.15: 11 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, V.106, F.113 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:H.62, C:I.64, C:V.106, C:F.113 Hydrogen bonds: C:P.1, C:I.64, B:Y.95, B:N.97 Salt bridges: C:K.32, C:K.32 pi-Stacking: B:Y.95 YZ9.16: 11 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, V.106, F.113 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:Y.95, B:Y.36, B:H.62, B:V.106, B:F.113 Hydrogen bonds: A:Y.95, A:N.97, B:P.1, B:I.64 pi-Stacking: A:Y.95 Salt bridges: B:K.32, B:K.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Orita, M. et al., Coumarin and chromen-4-one analogues as tautomerase inhibitors of macrophage migration inhibitory factor: discovery and X-ray crystallography. J.Med.Chem. (2001)

Release Date

2001-02-21

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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