SMTL ID : 5t36.1

Crystal structure of mPGES-1 bound to inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-trimer

Ligands

3 x 755: 4-chloro-2-[({(1S,2S)-2-[(2,2-dimethylpropanoyl)amino]cyclopentyl}methyl)amino]benzoic acid(Non-covalent)

755.1: 10 residues within 4Å: Chain A: P.126, S.129, V.130, T.133 Chain B: G.37, L.41, F.46, R.54, H.55 Ligands: GSH.2 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:P.126, A:V.130, B:L.41, B:F.46 Halogen bonds: A:T.133 Water bridges: B:R.54, B:H.55 Salt bridges: B:R.54, B:H.55 755.6: 10 residues within 4Å: Chain B: P.126, S.129, V.130, T.133 Chain C: G.37, L.41, F.46, R.54, H.55 Ligands: GSH.7 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:P.126, B:V.130, C:L.41, C:F.46 Halogen bonds: B:T.133 Water bridges: C:R.54, C:H.55 Salt bridges: C:R.54, C:H.55 755.11: 10 residues within 4Å: Chain A: G.37, L.41, F.46, R.54, H.55 Chain C: P.126, S.129, V.130, T.133 Ligands: GSH.12 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.41, A:F.46, C:P.126, C:V.130 Water bridges: A:R.54, A:H.55 Salt bridges: A:R.54, A:H.55 Halogen bonds: C:T.133

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: 755.1 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Water bridges: B:R.40, B:H.74, A:Y.132 Salt bridges: B:R.40 Hydrogen bonds: A:N.76, A:E.79, A:Y.119, A:Y.119, A:R.128 GSH.7: 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: 755.6 9 PLIP interactions: 6 interactions with chain B, 3 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:R.40, C:H.74 Salt bridges: C:R.40 GSH.12: 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: 755.11 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.76, C:E.79, C:Y.119, C:Y.119, C:R.128 Water bridges: C:Y.132, A:R.40, A:H.74 Salt bridges: A:R.40

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

BOG.3: 6 residues within 4Å: Chain A: L.137, S.141, L.144, Q.145, W.148 Ligands: PG4.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.137 Hydrogen bonds: A:S.141, A:Q.145, 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.28, A:V.31, A:I.35, A:T.116, A:L.120 Hydrogen bonds: A:K.122 BOG.8: 6 residues within 4Å: Chain B: L.137, S.141, L.144, Q.145, W.148 Ligands: PG4.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.137 Hydrogen bonds: B:S.141, B:Q.145, B:Q.145 Water bridges: B:S.141, B:S.141 BOG.9: 7 residues within 4Å: Chain B: K.28, V.31, I.35, T.116, L.120, G.121, K.122 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.28, B:V.31, B:I.35, B:T.116, B:L.120 Hydrogen bonds: B:K.122 BOG.13: 6 residues within 4Å: Chain C: L.137, S.141, L.144, Q.145, W.148 Ligands: PG4.15 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.137 Hydrogen bonds: C:S.141, C:Q.145, C:Q.145 Water bridges: C:S.141, C:S.141 BOG.14: 7 residues within 4Å: Chain C: K.28, V.31, I.35, T.116, L.120, G.121, K.122 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:K.28, C:V.31, C:I.35, C:T.116, C:L.120 Hydrogen bonds: C:K.122

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

PG4.5: 5 residues within 4Å: Chain A: M.103, H.104, L.137, S.141 Ligands: BOG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.141 Water bridges: A:S.141 PG4.10: 5 residues within 4Å: Chain B: M.103, H.104, L.137, S.141 Ligands: BOG.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.141 Water bridges: B:S.141 PG4.15: 5 residues within 4Å: Chain C: M.103, H.104, L.137, S.141 Ligands: BOG.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.141 Water bridges: C:S.141

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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