SMTL ID : 5t37.1

crystal structure of mPGES-1 bound to inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-trimer

Ligands

3 x 758: 2-chloro-5-{[(2,2-dimethylpropanoyl)amino]methyl}-N-(1H-imidazol-2-yl)benzamide(Non-covalent)

758.1: 14 residues within 4Å: Chain A: A.125, P.126, S.129, V.130, Y.132, T.133 Chain B: A.33, G.37, Q.38, L.41, D.51, H.55 Ligands: GSH.2, PG4.7 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.38, A:S.129, A:S.129, A:S.129 Hydrophobic interactions: A:Y.132 758.8: 14 residues within 4Å: Chain B: A.125, P.126, S.129, V.130, Y.132, T.133 Chain C: A.33, G.37, Q.38, L.41, D.51, H.55 Ligands: GSH.9, PG4.14 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.132 Hydrogen bonds: B:S.129, B:S.129, B:S.129, C:Q.38 758.15: 14 residues within 4Å: Chain A: A.33, G.37, Q.38, L.41, D.51, H.55 Chain C: A.125, P.126, S.129, V.130, Y.132, T.133 Ligands: GSH.16, PG4.21 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.132 Hydrogen bonds: C:S.129, C:S.129, C:S.129, A:Q.38

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: 758.1 9 PLIP interactions: 6 interactions with chain A, 3 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:R.40, B:H.74 Salt bridges: B:R.40 GSH.9: 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: 758.8 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.16: 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: 758.15 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: 7 residues within 4Å: Chain A: L.137, A.140, S.141, L.144, Q.145, W.148 Ligands: PG4.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.137, A:A.140 Hydrogen bonds: A:S.141, A:Q.145 BOG.4: 7 residues within 4Å: Chain A: K.28, V.31, I.35, 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:I.35, A:T.116 BOG.10: 7 residues within 4Å: Chain B: L.137, A.140, S.141, L.144, Q.145, W.148 Ligands: PG4.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.137, B:A.140 Hydrogen bonds: B:S.141, B:Q.145 BOG.11: 7 residues within 4Å: Chain B: K.28, V.31, I.35, 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:I.35, B:T.116 BOG.17: 7 residues within 4Å: Chain C: L.137, A.140, S.141, L.144, Q.145, W.148 Ligands: PG4.19 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.137, C:A.140 Hydrogen bonds: C:S.141, C:Q.145 BOG.18: 7 residues within 4Å: Chain C: K.28, V.31, I.35, 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:I.35, C:T.116

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

PG4.5: 6 residues within 4Å: Chain A: M.103, H.104, L.137, P.138, S.141 Ligands: BOG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.141 PG4.6: 4 residues within 4Å: Chain A: D.66, R.69, C.70, L.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.66 PG4.7: 3 residues within 4Å: Chain B: L.41, H.55 Ligands: 758.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.55 Water bridges: A:T.133 PG4.12: 6 residues within 4Å: Chain B: M.103, H.104, L.137, P.138, S.141 Ligands: BOG.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.141 PG4.13: 4 residues within 4Å: Chain B: D.66, R.69, C.70, L.120 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.66 PG4.14: 3 residues within 4Å: Chain C: L.41, H.55 Ligands: 758.8 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:T.133 Hydrogen bonds: C:H.55 PG4.19: 6 residues within 4Å: Chain C: M.103, H.104, L.137, P.138, S.141 Ligands: BOG.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.141 PG4.20: 4 residues within 4Å: Chain C: D.66, R.69, C.70, L.120 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.66 PG4.21: 3 residues within 4Å: Chain A: L.41, H.55 Ligands: 758.15 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:H.55 Water bridges: C:T.133

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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