SMTL ID : 3q7d.1

Structure of (R)-naproxen bound to mCOX-2.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 3 residues within 4Å: Chain A: Y.23, E.35, N.36 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.23, A:E.35, A:N.36 NAG.2: 7 residues within 4Å: Chain A: E.109, N.113, Y.116, R.185, F.189 Chain B: L.207 Ligands: NAG.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.113, A:R.185 Water bridges: A:R.185 NAG.3: 5 residues within 4Å: Chain A: Q.375, N.379, S.381, I.382, E.385 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.379, A:S.381 NAG.9: 2 residues within 4Å: Chain A: R.185 Ligands: NAG.2 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:L.207 Hydrophobic interactions: A:R.185 Hydrogen bonds: A:R.185 NAG.11: 4 residues within 4Å: Chain B: P.8, Y.23, E.35, N.36 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.35 Hydrogen bonds: B:E.35, B:N.36 NAG.12: 6 residues within 4Å: Chain A: L.207 Chain B: E.109, N.113, Y.116, R.185 Ligands: NAG.18 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.109, B:N.113, B:R.185 Water bridges: B:Y.116, B:Y.116, A:L.207 NAG.13: 6 residues within 4Å: Chain B: Y.371, Q.375, N.379, S.381, I.382, E.385 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.375, B:N.379, B:E.385 NAG.18: 2 residues within 4Å: Chain B: R.185 Ligands: NAG.12 No protein-ligand interaction detected (PLIP)

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.4: 18 residues within 4Å: Chain A: Y.117, A.168, Q.172, H.176, F.179, K.180, T.181, H.183, V.264, N.351, Y.354, H.355, W.356, H.357, L.360, L.377, V.416, Q.423 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.172, A:Q.172, A:F.179, A:V.264, A:Y.354, A:W.356, A:L.360, A:L.377, A:V.416, A:V.416 Hydrogen bonds: A:Y.117, A:T.181, A:N.351 Water bridges: A:F.179 Salt bridges: A:H.183 pi-Stacking: A:H.176 Metal complexes: A:H.357, H2O.2 HEM.14: 17 residues within 4Å: Chain B: A.168, A.171, Q.172, H.176, F.179, K.180, T.181, H.183, V.264, N.351, Y.354, H.355, H.357, L.360, L.377, V.416, A.419 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:A.171, B:Q.172, B:Q.172, B:F.179, B:V.264, B:Y.354, B:L.360, B:L.377, B:V.416, B:V.416 Hydrogen bonds: B:T.181, B:T.181, B:N.351 Salt bridges: B:H.183 pi-Stacking: B:H.176, B:H.355 Metal complexes: B:H.357

2 x NPX: (2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid(Non-covalent)

NPX.5: 14 residues within 4Å: Chain A: V.85, R.89, V.318, L.321, S.322, Y.324, F.350, Y.354, W.356, V.492, G.495, A.496, S.499, L.500 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.318, A:L.321, A:Y.324, A:A.496 Hydrogen bonds: A:Y.324 Salt bridges: A:R.89 NPX.15: 12 residues within 4Å: Chain B: R.89, V.318, L.321, S.322, Y.324, L.328, Y.354, W.356, G.495, A.496, S.499, L.500 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.318, B:L.321, B:Y.324, B:L.328, B:A.496 Hydrogen bonds: B:Y.324, B:Y.324 Salt bridges: B:R.89

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

BOG.6: 9 residues within 4Å: Chain A: E.148, K.149, L.152, R.153, R.154, R.407, I.411, E.455, E.459 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.148, A:L.152, A:L.152, A:I.411 Hydrogen bonds: A:R.407, A:E.455, A:E.455, A:E.459 Salt bridges: A:R.154 BOG.7: 9 residues within 4Å: Chain A: P.52, T.53, P.54, V.57, Y.84, S.88, R.89, L.92, E.493 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.84 Hydrogen bonds: A:P.52, A:S.88, A:S.88, A:S.88, A:E.493 Salt bridges: A:R.89 BOG.8: 3 residues within 4Å: Chain A: N.55, T.56, Y.59 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.56, A:Y.59 Hydrogen bonds: A:N.55 Water bridges: A:N.55 BOG.16: 9 residues within 4Å: Chain B: P.52, V.57, I.60, L.61, Y.84, S.88, R.89, L.92, E.493 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.57, B:I.60, B:L.61, B:Y.84, B:Y.84 Hydrogen bonds: B:P.52, B:S.88, B:S.88, B:S.88, B:R.89 Water bridges: B:Y.84 Salt bridges: B:R.89 BOG.17: 3 residues within 4Å: Chain B: N.55, T.56, Y.59 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.59 Hydrogen bonds: B:N.55

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 4 residues within 4Å: Chain A: F.174, F.350, Y.354, S.499 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: F.174, Y.354, S.499 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duggan, K.C. et al., (R)-Profens are substrate-selective inhibitors of endocannabinoid oxygenation by COX-2. Nat.Chem.Biol. (2011)

Release Date

2011-11-09

Peptides

Prostaglandin G/H synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin G/H synthase 2

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