SMTL ID : 5k0i.1

mpges1 bound to an inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

3 x 6PW: 1,5-anhydro-2,3,4-trideoxy-3-{[(4S)-3,3-dimethyl-1-(8-methylquinolin-2-yl)piperidine-4-carbonyl]amino}-D-erythro-hexitol(Non-covalent)

6PW.1: 12 residues within 4Å: Chain A: S.129, Y.132, T.133, Q.136 Chain B: Y.30, A.33, I.34, G.37, L.41, R.54, H.55 Ligands: GSH.2 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.30, B:Y.30, B:A.33, B:I.34, B:L.41, A:T.133, A:Q.136, A:Q.136 Hydrogen bonds: B:R.54, A:S.129 Water bridges: B:Q.38 6PW.7: 12 residues within 4Å: Chain B: S.129, Y.132, T.133, Q.136 Chain C: Y.30, A.33, I.34, G.37, L.41, R.54, H.55 Ligands: GSH.8 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:T.133, B:Q.136, B:Q.136, C:Y.30, C:Y.30, C:A.33, C:I.34, C:L.41 Hydrogen bonds: B:S.129, C:R.54 Water bridges: C:Q.38 6PW.13: 12 residues within 4Å: Chain A: Y.30, A.33, I.34, G.37, L.41, R.54, H.55 Chain C: S.129, Y.132, T.133, Q.136 Ligands: GSH.14 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Y.30, A:Y.30, A:A.33, A:I.34, A:L.41, C:T.133, C:Q.136, C:Q.136 Hydrogen bonds: A:R.54, C:S.129 Water bridges: 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: 6PW.1 8 PLIP interactions: 5 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: B:R.40, B:H.74 Salt bridges: B:R.40 GSH.8: 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: 6PW.7 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Water bridges: C:R.40, C:H.74 Salt bridges: C:R.40 Hydrogen bonds: B:N.76, B:E.79, B:Y.119, B:Y.119, B:R.128 GSH.14: 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: 6PW.13 8 PLIP interactions: 5 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: 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.137, A:A.140 Hydrogen bonds: A:S.141, A:Q.145, A:Q.145 BOG.4: 6 residues within 4Å: Chain A: K.28, V.31, T.116, L.120, G.121, K.122 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.28, A:V.31, A:T.116 BOG.9: 7 residues within 4Å: Chain B: L.137, A.140, S.141, L.144, Q.145, W.148 Ligands: PG4.11 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.137, B:A.140 Hydrogen bonds: B:S.141, B:Q.145, B:Q.145 BOG.10: 6 residues within 4Å: Chain B: K.28, V.31, T.116, L.120, G.121, K.122 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.28, B:V.31, B:T.116 BOG.15: 7 residues within 4Å: Chain C: L.137, A.140, S.141, L.144, Q.145, W.148 Ligands: PG4.17 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.137, C:A.140 Hydrogen bonds: C:S.141, C:Q.145, C:Q.145 BOG.16: 6 residues within 4Å: Chain C: K.28, V.31, T.116, L.120, G.121, K.122 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.28, C:V.31, C:T.116

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

PG4.5: 5 residues within 4Å: Chain A: M.103, H.104, 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 PG4.11: 5 residues within 4Å: Chain B: M.103, H.104, P.138, S.141 Ligands: BOG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.141 PG4.12: 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 PG4.17: 5 residues within 4Å: Chain C: M.103, H.104, P.138, S.141 Ligands: BOG.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.141 PG4.18: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuklish, S.L. et al., Characterization of 3,3-dimethyl substituted N-aryl piperidines as potent microsomal prostaglandin E synthase-1 inhibitors. Bioorg.Med.Chem.Lett. (2016)

Release Date

2016-09-14

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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