SMTL ID : 4yl1.1

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 4U8: 5-(4-tert-butylphenyl)-1-[4-(propan-2-yloxy)phenyl]-1H-indole-2-carboxylic acid(Non-covalent)

4U8.1: 12 residues within 4Å: Chain A: P.120, S.123, V.124, T.127, L.131 Chain B: G.31, R.34, L.35, F.40, R.48, H.49 Ligands: GSH.3 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:R.34, B:L.35, B:F.40, A:P.120, A:V.124, A:V.124, A:T.127 Water bridges: B:R.48, B:R.48, B:H.49 Salt bridges: B:R.48, B:H.49 4U8.7: 12 residues within 4Å: Chain B: P.120, S.123, V.124, T.127, L.131 Chain C: G.31, R.34, L.35, F.40, R.48, H.49 Ligands: GSH.9 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:P.120, B:V.124, B:V.124, B:T.127, C:R.34, C:L.35, C:F.40 Water bridges: C:R.48, C:R.48, C:H.49 Salt bridges: C:R.48, C:H.49 4U8.13: 12 residues within 4Å: Chain A: G.31, R.34, L.35, F.40, R.48, H.49 Chain C: P.120, S.123, V.124, T.127, L.131 Ligands: GSH.15 12 PLIP interactions: 4 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:P.120, C:V.124, C:V.124, C:T.127, A:R.34, A:L.35, A:F.40 Water bridges: A:R.48, A:R.48, A:H.49 Salt bridges: A:R.48, A:H.49

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

PEG.2: 5 residues within 4Å: Chain A: I.29, R.63, C.64, L.114 Ligands: BOG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.60 PEG.8: 5 residues within 4Å: Chain B: I.29, R.63, C.64, L.114 Ligands: BOG.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.60 PEG.14: 5 residues within 4Å: Chain C: I.29, R.63, C.64, L.114 Ligands: BOG.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.60

3 x GSH: GLUTATHIONE(Non-covalent)

GSH.3: 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: 4U8.1 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Water bridges: B:R.34, B:H.68, A:Y.126 Salt bridges: B:R.34 Hydrogen bonds: A:N.70, A:E.73, A:Y.113, A:Y.113, A:R.122 GSH.9: 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: 4U8.7 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain B Water bridges: C:R.34, C:H.68, B:Y.126 Salt bridges: C:R.34 Hydrogen bonds: B:N.70, B:E.73, B:Y.113, B:Y.113, B:R.122 GSH.15: 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: 4U8.13 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.70, C:E.73, C:Y.113, C:Y.113, C:R.122 Water bridges: C:Y.126, A:R.34, A:H.68 Salt bridges: A:R.34

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

BOG.4: 6 residues within 4Å: Chain A: A.134, S.135, L.138, Q.139, W.142 Ligands: PG4.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.134 Hydrogen bonds: A:S.135, A:Q.139, A:Q.139 Water bridges: A:S.135, A:S.135 BOG.5: 8 residues within 4Å: Chain A: K.22, V.25, I.29, T.110, L.114, G.115, K.116 Ligands: PEG.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.22, A:V.25, A:T.110 BOG.10: 6 residues within 4Å: Chain B: A.134, S.135, L.138, Q.139, W.142 Ligands: PG4.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.134 Hydrogen bonds: B:S.135, B:Q.139, B:Q.139 Water bridges: B:S.135, B:S.135 BOG.11: 8 residues within 4Å: Chain B: K.22, V.25, I.29, T.110, L.114, G.115, K.116 Ligands: PEG.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.22, B:V.25, B:T.110 BOG.16: 6 residues within 4Å: Chain C: A.134, S.135, L.138, Q.139, W.142 Ligands: PG4.18 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.134 Hydrogen bonds: C:S.135, C:Q.139, C:Q.139 Water bridges: C:S.135, C:S.135 BOG.17: 8 residues within 4Å: Chain C: K.22, V.25, I.29, T.110, L.114, G.115, K.116 Ligands: PEG.14 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.22, C:V.25, C:T.110

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

PG4.6: 7 residues within 4Å: Chain A: V.94, M.97, H.98, L.131, P.132, S.135 Ligands: BOG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.135 PG4.12: 7 residues within 4Å: Chain B: V.94, M.97, H.98, L.131, P.132, S.135 Ligands: BOG.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.135 PG4.18: 7 residues within 4Å: Chain C: V.94, M.97, H.98, L.131, P.132, S.135 Ligands: BOG.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: 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

2015-06-10

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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