SMTL ID : 6vl4.1

Crystal Structure of mPGES-1 bound to DG-031

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-trimer

Ligands

3 x QY1: (2R)-cyclopentyl{4-[(quinolin-2-yl)methoxy]phenyl}acetic acid(Non-covalent)

QY1.1: 12 residues within 4Å: Chain A: R.128, S.129, Y.132, T.133, Q.136, A.140 Chain B: Y.30, A.33, I.34, G.37, R.40, D.51 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.132, A:Y.132, A:Q.136, A:Q.136, A:Q.136, A:A.140, B:Y.30, B:I.34, B:I.34 Hydrogen bonds: A:S.129 Water bridges: A:R.128, A:R.128, A:R.128 Salt bridges: A:R.128 QY1.5: 12 residues within 4Å: Chain B: R.128, S.129, Y.132, T.133, Q.136, A.140 Chain C: Y.30, A.33, I.34, G.37, R.40, D.51 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:Y.132, B:Y.132, B:Q.136, B:Q.136, B:Q.136, B:A.140, C:Y.30, C:I.34, C:I.34 Hydrogen bonds: B:S.129 Water bridges: B:R.128, B:R.128, B:R.128 Salt bridges: B:R.128 QY1.9: 12 residues within 4Å: Chain A: Y.30, A.33, I.34, G.37, R.40, D.51 Chain C: R.128, S.129, Y.132, T.133, Q.136, A.140 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:Y.132, C:Y.132, C:Q.136, C:Q.136, C:Q.136, C:A.140, A:Y.30, A:I.34, A:I.34 Hydrogen bonds: C:S.129 Water bridges: C:R.128, C:R.128, C:R.128 Salt bridges: C:R.128

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

BOG.2: 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.6: 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.10: 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)

PG4.3: 3 residues within 4Å: Chain A: M.103, L.137, S.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.141 Water bridges: A:H.104, A:S.141 PG4.4: 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 PG4.7: 3 residues within 4Å: Chain B: M.103, L.137, S.141 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.141 Water bridges: B:H.104, B:S.141 PG4.8: 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 PG4.11: 3 residues within 4Å: Chain C: M.103, L.137, S.141 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.141 Water bridges: C:H.104, C:S.141 PG4.12: 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

Ho, J.D. et al., Structure-based, multi-targeted drug discovery approach to eicosanoid inhibition: Dual inhibitors of mPGES-1 and 5-lipoxygenase activating protein (FLAP). Biochim Biophys Acta Gen Subj (2020)

Release Date

2020-12-02

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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