SMTL ID : 4yk5.1

Crystal Structures of mPGES-1 Inhibitor Complexes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-trimer

Ligands

3 x 4DV: 3-[1-(4-chlorobenzyl)-5-(2-fluoro-2'-methylbiphenyl-4-yl)-3-methyl-1H-indol-2-yl]-2,2-dimethylpropanoic acid(Non-covalent)

4DV.1: 18 residues within 4Å: Chain A: P.126, S.129, V.130, Y.132, T.133, Q.136, L.137, A.140 Chain B: Y.30, I.34, G.37, R.40, L.41, F.46, R.54, H.55 Ligands: GSH.3, JZR.4 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:Y.132, A:T.133, A:Q.136, A:L.137, A:A.140, B:Y.30, B:Y.30, B:I.34, B:I.34, B:L.41, B:L.41 Hydrogen bonds: B:H.55 Water bridges: B:R.54 Salt bridges: B:R.54 4DV.7: 18 residues within 4Å: Chain B: P.126, S.129, V.130, Y.132, T.133, Q.136, L.137, A.140 Chain C: Y.30, I.34, G.37, R.40, L.41, F.46, R.54, H.55 Ligands: GSH.9, JZR.10 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:Y.30, C:Y.30, C:I.34, C:I.34, C:L.41, C:L.41, B:Y.132, B:T.133, B:Q.136, B:L.137, B:A.140 Hydrogen bonds: C:H.55 Water bridges: C:R.54 Salt bridges: C:R.54 4DV.13: 18 residues within 4Å: Chain A: Y.30, I.34, G.37, R.40, L.41, F.46, R.54, H.55 Chain C: P.126, S.129, V.130, Y.132, T.133, Q.136, L.137, A.140 Ligands: GSH.15, JZR.16 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:Y.30, A:Y.30, A:I.34, A:I.34, A:L.41, A:L.41, C:Y.132, C:T.133, C:Q.136, C:L.137, C:A.140 Hydrogen bonds: A:H.55 Water bridges: A:R.54 Salt bridges: A:R.54

3 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.2: 5 residues within 4Å: Chain A: I.35, D.66, R.69, C.70, L.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.66 Water bridges: A:R.42 PG0.8: 5 residues within 4Å: Chain B: I.35, D.66, R.69, C.70, L.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.66 Water bridges: B:R.42 PG0.14: 5 residues within 4Å: Chain C: I.35, D.66, R.69, C.70, L.120 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.66 Water bridges: C:R.42

3 x GSH: GLUTATHIONE(Non-covalent)

GSH.3: 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: 4DV.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: 4DV.7 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.15: 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: 4DV.13 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

3 x JZR: hexyl beta-D-glucopyranoside(Non-covalent)

JZR.4: 8 residues within 4Å: Chain A: L.137, A.140, S.141, L.144, Q.145, W.148 Ligands: 4DV.1, PG4.6 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 JZR.10: 8 residues within 4Å: Chain B: L.137, A.140, S.141, L.144, Q.145, W.148 Ligands: 4DV.7, PG4.12 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 JZR.16: 8 residues within 4Å: Chain C: L.137, A.140, S.141, L.144, Q.145, W.148 Ligands: 4DV.13, PG4.18 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

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

BOG.5: 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.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: 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

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

PG4.6: 6 residues within 4Å: Chain A: M.103, H.104, L.137, P.138, S.141 Ligands: JZR.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.141 PG4.12: 6 residues within 4Å: Chain B: M.103, H.104, L.137, P.138, S.141 Ligands: JZR.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.141 PG4.18: 6 residues within 4Å: Chain C: M.103, H.104, L.137, P.138, S.141 Ligands: JZR.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.141

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

2015-07-15

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