SMTL ID : 5bqg.1

Crystal Structure of mPGES-1 Bound to an Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-trimer

Ligands

3 x 4UJ: 2-chloro-N-(4-phenyl-1,3-thiazol-2-yl)benzamide(Non-covalent)

4UJ.1: 9 residues within 4Å: Chain A: P.126, S.129, V.130, T.133 Chain B: L.41, F.46, D.51, H.55 Ligands: GSH.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.130, A:T.133, B:L.41, B:F.46 Hydrogen bonds: A:S.129 Water bridges: A:S.129 4UJ.7: 9 residues within 4Å: Chain B: P.126, S.129, V.130, T.133 Chain C: L.41, F.46, D.51, H.55 Ligands: GSH.8 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:V.130, B:T.133, C:L.41, C:F.46 Hydrogen bonds: B:S.129 Water bridges: B:S.129 4UJ.13: 9 residues within 4Å: Chain A: L.41, F.46, D.51, H.55 Chain C: P.126, S.129, V.130, T.133 Ligands: GSH.14 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:V.130, C:T.133, A:L.41, A:F.46 Hydrogen bonds: C:S.129 Water bridges: C:S.129

3 x GSH: GLUTATHIONE(Non-covalent)

GSH.2: 14 residues within 4Å: Chain A: R.72, R.75, 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: 4UJ.1 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A Water bridges: B:H.74, A:Y.132 Salt bridges: B:R.40, A:R.75, A:R.75 Hydrogen bonds: A:R.75, A:N.76, A:E.79, A:Y.119, A:Y.119, A:R.128 GSH.8: 14 residues within 4Å: Chain B: R.72, R.75, 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: 4UJ.7 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.75, 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: B:R.75, B:R.75, C:R.40 GSH.14: 14 residues within 4Å: Chain A: A.33, T.36, R.40, L.71 Chain C: R.72, R.75, N.76, E.79, H.115, Y.119, R.128, S.129, Y.132 Ligands: 4UJ.13 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain C Water bridges: A:H.74, C:Y.132 Salt bridges: A:R.40, C:R.75, C:R.75 Hydrogen bonds: C:R.75, C:N.76, C:E.79, C:Y.119, C:Y.119, C:R.128

3 x JZR: hexyl beta-D-glucopyranoside(Non-covalent)

JZR.3: 6 residues within 4Å: Chain A: A.140, S.141, L.144, Q.145, W.148 Ligands: PGE.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.140 Hydrogen bonds: A:S.141, A:Q.145, A:Q.145 Water bridges: A:S.141, A:S.141 JZR.9: 6 residues within 4Å: Chain B: A.140, S.141, L.144, Q.145, W.148 Ligands: PGE.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.140 Hydrogen bonds: B:S.141, B:Q.145, B:Q.145 Water bridges: B:S.141, B:S.141 JZR.15: 6 residues within 4Å: Chain C: A.140, S.141, L.144, Q.145, W.148 Ligands: PGE.17 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.140 Hydrogen bonds: C:S.141, C:Q.145, C:Q.145 Water bridges: C:S.141, C:S.141

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

BOG.4: 6 residues within 4Å: Chain A: K.28, V.31, T.116, L.120, G.121, K.122 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.28, A:V.31, A:T.116, A:L.120 BOG.10: 6 residues within 4Å: Chain B: K.28, V.31, T.116, L.120, G.121, K.122 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.28, B:V.31, B:T.116, B:L.120 BOG.16: 6 residues within 4Å: Chain C: K.28, V.31, T.116, L.120, G.121, K.122 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.28, C:V.31, C:T.116, C:L.120

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 4 residues within 4Å: Chain A: M.103, H.104, P.138 Ligands: JZR.3 No protein-ligand interaction detected (PLIP) PGE.11: 4 residues within 4Å: Chain B: M.103, H.104, P.138 Ligands: JZR.9 No protein-ligand interaction detected (PLIP) PGE.17: 4 residues within 4Å: Chain C: M.103, H.104, P.138 Ligands: JZR.15 No protein-ligand interaction detected (PLIP)

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 3 residues within 4Å: Chain A: D.66, R.69, L.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.66 PEG.12: 3 residues within 4Å: Chain B: D.66, R.69, L.120 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.66 PEG.18: 3 residues within 4Å: Chain C: D.66, R.69, L.120 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.66

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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