SMTL ID : 4yl3.1

Crystal Structures of mPGES-1 Inhibitor Complexes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-trimer

Ligands

3 x 4U9: 5-[4-bromo-2-(2-chloro-6-fluorophenyl)-1H-imidazol-5-yl]-2-{[4-(trifluoromethyl)phenyl]ethynyl}pyridine(Non-covalent)

4U9.1: 14 residues within 4Å: Chain A: P.120, S.123, V.124, T.127, L.128, L.131 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:T.127, B:L.35, B:F.40 Hydrogen bonds: A:S.123, A:S.123 Water bridges: A:T.127 Halogen bonds: B:R.48 4U9.6: 14 residues within 4Å: Chain B: P.120, S.123, V.124, T.127, L.128, L.131 Chain C: G.31, R.34, L.35, F.40, D.45, R.48, H.49 Ligands: GSH.7 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:T.127, C:L.35, C:F.40 Hydrogen bonds: B:S.123, B:S.123 Water bridges: B:T.127 Halogen bonds: C:R.48 4U9.11: 14 residues within 4Å: Chain A: G.31, R.34, L.35, F.40, D.45, R.48, H.49 Chain C: P.120, S.123, V.124, T.127, L.128, L.131 Ligands: GSH.12 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.35, A:F.40, C:T.127 Halogen bonds: A:R.48 Hydrogen bonds: C:S.123, C:S.123 Water bridges: C:T.127

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: 4U9.1 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:N.42, B:H.68, B:H.68 Hydrophobic interactions: B:T.30 Salt bridges: B:R.34 GSH.7: 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: 4U9.6 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:N.42, C:H.68, C:H.68 Hydrophobic interactions: C:T.30 Salt bridges: C:R.34 GSH.12: 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: 4U9.11 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:N.70, C:E.73, C:Y.113, C:Y.113, C:R.122 Water bridges: C:N.70, C:Y.126, A:R.34, A:N.42, A:H.68, A:H.68 Hydrophobic interactions: A:T.30 Salt bridges: A:R.34

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

BOG.3: 7 residues within 4Å: Chain A: L.131, A.134, S.135, L.138, Q.139, W.142 Ligands: PG4.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.131, A:A.134 Hydrogen bonds: A:S.135, A:Q.139 Water bridges: A:S.135, A:S.135 BOG.4: 6 residues within 4Å: Chain A: K.22, V.25, T.110, L.114, G.115, K.116 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.22, A:V.25, A:T.110 Water bridges: A:L.114 BOG.8: 7 residues within 4Å: Chain B: L.131, A.134, S.135, L.138, Q.139, W.142 Ligands: PG4.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.131, B:A.134 Hydrogen bonds: B:S.135, B:Q.139 Water bridges: B:S.135, B:S.135 BOG.9: 6 residues within 4Å: Chain B: K.22, V.25, T.110, L.114, G.115, K.116 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.22, B:V.25, B:T.110 Water bridges: B:L.114 BOG.13: 7 residues within 4Å: Chain C: L.131, A.134, S.135, L.138, Q.139, W.142 Ligands: PG4.15 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.131, C:A.134 Hydrogen bonds: C:S.135, C:Q.139 Water bridges: C:S.135, C:S.135 BOG.14: 6 residues within 4Å: Chain C: K.22, V.25, T.110, L.114, G.115, K.116 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.22, C:V.25, C:T.110 Water bridges: C:L.114

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

PG4.5: 7 residues within 4Å: Chain A: M.97, H.98, V.101, L.131, P.132, S.135 Ligands: BOG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.135 Water bridges: A:H.98, A:S.135 PG4.10: 7 residues within 4Å: Chain B: M.97, H.98, V.101, L.131, P.132, S.135 Ligands: BOG.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.135 Water bridges: B:H.98, B:S.135 PG4.15: 7 residues within 4Å: Chain C: M.97, H.98, V.101, L.131, P.132, S.135 Ligands: BOG.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.135 Water bridges: C:H.98, C:S.135

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

2015-07-08

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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