SMTL ID : 5tl9.1

crystal structure of mPGES-1 bound to inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-trimer

Ligands

3 x 7DN: 2-{2-[(1S,2S)-2-{[1-(8-methylquinolin-2-yl)piperidine-4-carbonyl]amino}cyclopentyl]ethyl}benzoic acid(Non-covalent)

7DN.1: 17 residues within 4Å: Chain A: Y.30, A.33, I.34, G.37, R.40, L.41, F.46, R.54, H.55 Chain C: P.126, S.129, V.130, Y.132, T.133, Q.136 Ligands: PG4.5, GSH.16 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:Y.30, A:Y.30, A:A.33, A:I.34, A:R.40, A:F.46, C:P.126, C:V.130, C:T.133, C:Q.136, C:Q.136 Water bridges: A:Q.38 Salt bridges: A:R.54, A:H.55 7DN.8: 17 residues within 4Å: Chain A: P.126, S.129, V.130, Y.132, T.133, Q.136 Chain B: Y.30, A.33, I.34, G.37, R.40, L.41, F.46, R.54, H.55 Ligands: GSH.2, PG4.12 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.30, B:Y.30, B:A.33, B:I.34, B:R.40, B:F.46, A:P.126, A:V.130, A:T.133, A:Q.136, A:Q.136 Water bridges: B:Q.38 Salt bridges: B:R.54, B:H.55 7DN.15: 17 residues within 4Å: Chain B: P.126, S.129, V.130, Y.132, T.133, Q.136 Chain C: Y.30, A.33, I.34, G.37, R.40, L.41, F.46, R.54, H.55 Ligands: GSH.9, PG4.19 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:Y.30, C:Y.30, C:A.33, C:I.34, C:R.40, C:F.46, B:P.126, B:V.130, B:T.133, B:Q.136, B:Q.136 Water bridges: C:Q.38 Salt bridges: C:R.54, C:H.55

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: 7DN.8 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.75, A:N.76, A:E.79, A:Y.119, A:Y.119, A:R.128 Salt bridges: A:R.75, A:R.75, B:R.40 Hydrophobic interactions: B:T.36 Water bridges: B:H.74 GSH.9: 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: 7DN.15 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.75, B:N.76, B:E.79, B:Y.119, B:Y.119, B:R.128 Salt bridges: B:R.75, B:R.75, C:R.40 Hydrophobic interactions: C:T.36 Water bridges: C:H.74 GSH.16: 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: 7DN.1 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.75, C:N.76, C:E.79, C:Y.119, C:Y.119, C:R.128 Salt bridges: C:R.75, C:R.75, A:R.40 Hydrophobic interactions: A:T.36 Water bridges: A:H.74

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: PG4.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.141, A:Q.145, A:Q.145 Water bridges: A:S.141, A:S.141 JZR.10: 6 residues within 4Å: Chain B: A.140, S.141, L.144, Q.145, W.148 Ligands: PG4.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.141, B:Q.145, B:Q.145 Water bridges: B:S.141, B:S.141 JZR.17: 6 residues within 4Å: Chain C: A.140, S.141, L.144, Q.145, W.148 Ligands: PG4.20 5 PLIP interactions: 5 interactions with chain C 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: 8 residues within 4Å: Chain A: K.28, V.31, I.35, T.116, L.120, G.121, K.122 Ligands: PEG.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.28, A:V.31, A:I.35, A:T.116 Water bridges: A:K.122 BOG.11: 8 residues within 4Å: Chain B: K.28, V.31, I.35, T.116, L.120, G.121, K.122 Ligands: PEG.14 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.28, B:V.31, B:I.35, B:T.116 Water bridges: B:K.122 BOG.18: 8 residues within 4Å: Chain C: K.28, V.31, I.35, T.116, L.120, G.121, K.122 Ligands: PEG.21 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:K.28, C:V.31, C:I.35, C:T.116 Water bridges: C:K.122

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

PG4.5: 4 residues within 4Å: Chain A: I.34, Q.38, L.41 Ligands: 7DN.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.38, A:Q.38 PG4.6: 6 residues within 4Å: Chain A: M.103, H.104, L.137, P.138, S.141 Ligands: JZR.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.141 PG4.12: 4 residues within 4Å: Chain B: I.34, Q.38, L.41 Ligands: 7DN.8 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.38, B:Q.38 PG4.13: 6 residues within 4Å: Chain B: M.103, H.104, L.137, P.138, S.141 Ligands: JZR.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.141 PG4.19: 4 residues within 4Å: Chain C: I.34, Q.38, L.41 Ligands: 7DN.15 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.38, C:Q.38 PG4.20: 6 residues within 4Å: Chain C: M.103, H.104, L.137, P.138, S.141 Ligands: JZR.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.141

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

PEG.7: 6 residues within 4Å: Chain A: I.35, D.66, R.69, C.70, L.120 Ligands: BOG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.66 PEG.14: 6 residues within 4Å: Chain B: I.35, D.66, R.69, C.70, L.120 Ligands: BOG.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.66 PEG.21: 6 residues within 4Å: Chain C: I.35, D.66, R.69, C.70, L.120 Ligands: BOG.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Partridge, K.M. et al., Discovery and characterization of [(cyclopentyl)ethyl]benzoic acid inhibitors of microsomal prostaglandin E synthase-1. Bioorg. Med. Chem. Lett. (2017)

Release Date

2017-03-01

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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