SMTL ID : 4yl0.1

Crystal Structures of mPGES-1 Inhibitor Complexes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-trimer

Ligands

3 x 4DZ: 2-(9-chloro-1H-phenanthro[9,10-d]imidazol-2-yl)benzene-1,3-dicarbonitrile(Non-covalent)

4DZ.1: 13 residues within 4Å: Chain A: A.119, P.120, S.123, V.124, T.127 Chain B: G.31, R.34, L.35, F.40, D.45, R.48, H.49 Ligands: GSH.2 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.120, A:P.120, A:V.124, B:F.40 Hydrogen bonds: A:S.123, B:H.49 Water bridges: B:Q.32 4DZ.7: 13 residues within 4Å: Chain B: A.119, P.120, S.123, V.124, T.127 Chain C: G.31, R.34, L.35, F.40, D.45, R.48, H.49 Ligands: GSH.8 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.40, B:P.120, B:P.120, B:V.124 Hydrogen bonds: C:H.49, B:S.123 Water bridges: C:Q.32 4DZ.13: 13 residues within 4Å: Chain A: G.31, R.34, L.35, F.40, D.45, R.48, H.49 Chain C: A.119, P.120, S.123, V.124, T.127 Ligands: GSH.14 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:F.40, C:P.120, C:P.120, C:V.124 Hydrogen bonds: A:H.49, C:S.123 Water bridges: A:Q.32

3 x GSH: GLUTATHIONE(Non-covalent)

GSH.2: 13 residues within 4Å: Chain A: R.66, N.70, E.73, H.109, Y.113, R.122, S.123, Y.126 Chain B: A.27, T.30, R.34, L.65 Ligands: 4DZ.1 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:N.70, A:E.73, A:Y.113, A:Y.113, A:R.122 Water bridges: A:N.70, A:Y.126, B:R.34, B:R.34, B:N.42, B:N.42, B:H.68 Salt bridges: B:R.34 GSH.8: 13 residues within 4Å: Chain B: R.66, N.70, E.73, H.109, Y.113, R.122, S.123, Y.126 Chain C: A.27, T.30, R.34, L.65 Ligands: 4DZ.7 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:N.70, B:E.73, B:Y.113, B:Y.113, B:R.122 Water bridges: B:N.70, B:Y.126, C:R.34, C:R.34, C:N.42, C:N.42, C:H.68 Salt bridges: C:R.34 GSH.14: 13 residues within 4Å: Chain A: A.27, T.30, R.34, L.65 Chain C: R.66, N.70, E.73, H.109, Y.113, R.122, S.123, Y.126 Ligands: 4DZ.13 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain C Water bridges: A:R.34, A:R.34, A:N.42, A:N.42, A:H.68, C:N.70, C:Y.126 Salt bridges: A:R.34 Hydrogen bonds: C:N.70, C:E.73, C:Y.113, C:Y.113, C:R.122

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

BOG.3: 6 residues within 4Å: Chain A: A.134, S.135, L.138, Q.139, W.142 Ligands: PG4.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.134 Hydrogen bonds: A:S.135, A:Q.139, A:W.142 Water bridges: A:S.135, A:S.135 BOG.4: 8 residues within 4Å: Chain A: K.22, V.25, I.29, T.110, L.114, G.115, K.116 Ligands: PEG.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.22, A:V.25, A:I.29, A:T.110 Hydrogen bonds: A:K.116 BOG.9: 6 residues within 4Å: Chain B: A.134, S.135, L.138, Q.139, W.142 Ligands: PG4.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.134 Hydrogen bonds: B:S.135, B:Q.139, B:W.142 Water bridges: B:S.135, B:S.135 BOG.10: 8 residues within 4Å: Chain B: K.22, V.25, I.29, T.110, L.114, G.115, K.116 Ligands: PEG.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.22, B:V.25, B:I.29, B:T.110 Hydrogen bonds: B:K.116 BOG.15: 6 residues within 4Å: Chain C: A.134, S.135, L.138, Q.139, W.142 Ligands: PG4.17 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.134 Hydrogen bonds: C:S.135, C:Q.139, C:W.142 Water bridges: C:S.135, C:S.135 BOG.16: 8 residues within 4Å: Chain C: K.22, V.25, I.29, T.110, L.114, G.115, K.116 Ligands: PEG.18 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:K.22, C:V.25, C:I.29, C:T.110 Hydrogen bonds: C:K.116

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

PG4.5: 5 residues within 4Å: Chain A: M.97, H.98, P.132, S.135 Ligands: BOG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.135 PG4.11: 5 residues within 4Å: Chain B: M.97, H.98, P.132, S.135 Ligands: BOG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.135 PG4.17: 5 residues within 4Å: Chain C: M.97, H.98, P.132, S.135 Ligands: BOG.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.135

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

PEG.6: 4 residues within 4Å: Chain A: D.60, R.63, L.114 Ligands: BOG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.60 PEG.12: 4 residues within 4Å: Chain B: D.60, R.63, L.114 Ligands: BOG.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.60 PEG.18: 4 residues within 4Å: Chain C: D.60, R.63, L.114 Ligands: BOG.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luz, J.G. et al., Crystal Structures of mPGES-1 Inhibitor Complexes Form a Basis for the Rational Design of Potent Analgesic and Anti-Inflammatory Therapeutics. J.Med.Chem. (2015)

Release Date

2015-06-10

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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