SMTL ID : 5bqh.1

Discovery of a Potent and Selective mPGES-1 Inhibitor for the Treatment of Pain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

3 x 4UK: N-[4-(4-chlorophenyl)-1H-imidazol-2-yl]-2-(difluoromethyl)-5-{[(2-methylpropanoyl)amino]methyl}benzamide(Non-covalent)

4UK.1: 13 residues within 4Å: Chain A: A.125, P.126, S.129, V.130, Y.132, T.133 Chain B: A.33, G.37, L.41, D.51, R.54, H.55 Ligands: GSH.2 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.130, A:Y.132, A:T.133 Hydrogen bonds: A:S.129, A:S.129, B:R.54 Water bridges: B:Q.38, B:R.54, B:R.54 Halogen bonds: B:D.51 4UK.7: 13 residues within 4Å: Chain B: A.125, P.126, S.129, V.130, Y.132, T.133 Chain C: A.33, G.37, L.41, D.51, R.54, H.55 Ligands: GSH.8 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:V.130, B:Y.132, B:T.133 Hydrogen bonds: B:S.129, B:S.129, C:R.54 Water bridges: C:Q.38, C:R.54, C:R.54 Halogen bonds: C:D.51 4UK.13: 13 residues within 4Å: Chain A: A.33, G.37, L.41, D.51, R.54, H.55 Chain C: A.125, P.126, S.129, V.130, Y.132, T.133 Ligands: GSH.14 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:V.130, C:Y.132, C:T.133 Hydrogen bonds: C:S.129, C:S.129, A:R.54 Water bridges: A:Q.38, A:R.54, A:R.54 Halogen bonds: A:D.51

3 x GSH: GLUTATHIONE(Non-covalent)

GSH.2: 13 residues within 4Å: Chain A: R.72, N.76, E.79, H.115, Y.119, R.128, S.129, Y.132 Chain B: A.33, T.36, R.40, L.71 Ligands: 4UK.1 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.76, A:E.79, A:Y.119, A:Y.119, A:R.128 Water bridges: A:Y.132, B:H.74 Salt bridges: B:R.40 GSH.8: 13 residues within 4Å: Chain B: R.72, N.76, E.79, H.115, Y.119, R.128, S.129, Y.132 Chain C: A.33, T.36, R.40, L.71 Ligands: 4UK.7 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.76, B:E.79, B:Y.119, B:Y.119, B:R.128 Water bridges: B:Y.132, C:H.74 Salt bridges: C:R.40 GSH.14: 13 residues within 4Å: Chain A: A.33, T.36, R.40, L.71 Chain C: R.72, N.76, E.79, H.115, Y.119, R.128, S.129, Y.132 Ligands: 4UK.13 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C Water bridges: A:H.74, C:Y.132 Salt bridges: A:R.40 Hydrogen bonds: C:N.76, C:E.79, C:Y.119, C:Y.119, C:R.128

6 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.3: 4 residues within 4Å: Chain A: S.141, Q.145, W.148 Ligands: PG4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.141, A:Q.145 Water bridges: A:S.141, A:S.141 BOG.4: 7 residues within 4Å: Chain A: K.28, V.31, I.35, T.116, L.120, G.121, K.122 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.28, A:V.31, A:I.35, A:T.116, A:L.120 BOG.9: 4 residues within 4Å: Chain B: S.141, Q.145, W.148 Ligands: PG4.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.141, B:Q.145 Water bridges: B:S.141, B:S.141 BOG.10: 7 residues within 4Å: Chain B: K.28, V.31, I.35, T.116, L.120, G.121, K.122 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.28, B:V.31, B:I.35, B:T.116, B:L.120 BOG.15: 4 residues within 4Å: Chain C: S.141, Q.145, W.148 Ligands: PG4.17 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.141, C:Q.145 Water bridges: C:S.141, C:S.141 BOG.16: 7 residues within 4Å: Chain C: K.28, V.31, I.35, T.116, L.120, G.121, K.122 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:K.28, C:V.31, C:I.35, C:T.116, C:L.120

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 4 residues within 4Å: Chain A: M.103, H.104, P.138 Ligands: BOG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.141 PG4.11: 4 residues within 4Å: Chain B: M.103, H.104, P.138 Ligands: BOG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.141 PG4.17: 4 residues within 4Å: Chain C: M.103, H.104, P.138 Ligands: BOG.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.141

3 x 1KA: (2-hydroxyethoxy)acetaldehyde(Non-covalent)

1KA.6: 5 residues within 4Å: Chain A: I.35, D.66, R.69, C.70, L.120 No protein-ligand interaction detected (PLIP) 1KA.12: 5 residues within 4Å: Chain B: I.35, D.66, R.69, C.70, L.120 No protein-ligand interaction detected (PLIP) 1KA.18: 5 residues within 4Å: Chain C: I.35, D.66, R.69, C.70, L.120 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiffler, M.A. et al., Discovery and Characterization of 2-Acylaminoimidazole Microsomal Prostaglandin E Synthase-1 Inhibitors. J.Med.Chem. (2016)

Release Date

2016-04-13

Peptides

Prostaglandin E synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
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Prostaglandin E synthase

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