SMTL ID : 3nt1.1

High resolution structure of naproxen:COX-2 complex.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: E.109, N.113, Y.116, R.185, F.189 Chain B: L.207 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:D.208, B:D.208 Hydrogen bonds: A:R.185 NAG-NAG.2: 6 residues within 4Å: Chain A: L.207 Chain B: E.109, N.113, Y.116, R.185, F.189 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.185 Water bridges: A:D.208, A:D.208

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 4 residues within 4Å: Chain A: S.6, Y.23, E.35, N.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.23 Water bridges: A:N.36 NAG.4: 5 residues within 4Å: Chain A: Q.375, N.379, S.381, I.382, E.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.379 NAG.11: 4 residues within 4Å: Chain B: Q.375, N.379, S.381, I.382 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.379, B:N.379 NAG.15: 4 residues within 4Å: Chain B: P.8, Y.23, E.35, N.36 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.35 Hydrogen bonds: B:Y.23, B:E.35, B:N.36 Water bridges: B:S.6, B:S.6, B:T.38

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

BOG.5: 7 residues within 4Å: Chain A: E.148, K.149, R.153, R.154, R.407, E.455, E.459 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.149, A:K.149, A:R.154, A:R.407, A:R.407, A:E.455, A:E.459, A:E.459 Salt bridges: A:R.154 BOG.8: 11 residues within 4Å: Chain A: K.51, P.52, T.53, P.54, V.57, I.60, Y.84, V.85, S.88, R.89, E.493 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.60, A:Y.84, A:Y.84 Hydrogen bonds: A:K.51, A:K.51, A:P.52, A:S.88, A:S.88, A:S.88, A:R.89 Water bridges: A:R.89, A:S.440 Salt bridges: A:R.89 BOG.9: 3 residues within 4Å: Chain A: N.55, T.56, Y.59 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.56, A:Y.59 Hydrogen bonds: A:N.55 Water bridges: A:N.55, A:E.449 BOG.13: 13 residues within 4Å: Chain B: K.51, P.52, T.53, P.54, V.57, I.60, L.61, Y.84, V.85, S.88, R.89, L.92, E.493 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.57, B:I.60, B:L.61, B:Y.84, B:V.85 Hydrogen bonds: B:K.51, B:K.51, B:P.52, B:S.88, B:S.88, B:S.88, B:R.89, B:E.493 Water bridges: B:Y.84, B:R.89, B:R.89 Salt bridges: B:R.89

2 x NPS: (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid(Non-covalent)

NPS.6: 13 residues within 4Å: Chain A: V.85, R.89, V.318, L.321, Y.324, L.328, Y.354, W.356, V.492, G.495, A.496, S.499, L.500 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.318, A:L.321, A:Y.324, A:L.328, A:V.492, A:A.496 Hydrogen bonds: A:Y.324 Salt bridges: A:R.89 NPS.12: 13 residues within 4Å: Chain B: V.85, R.89, V.318, L.321, Y.324, L.328, Y.354, W.356, V.492, G.495, A.496, S.499, L.500 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.318, B:L.321, B:Y.324, B:L.328, B:V.492, B:A.496 Salt bridges: B:R.89

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

HEM.7: 18 residues within 4Å: Chain A: Y.117, A.168, F.169, A.171, Q.172, H.176, F.179, K.180, T.181, H.183, N.351, Y.354, H.355, W.356, H.357, L.360, V.416, Q.423 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.169, A:A.171, A:Q.172, A:Q.172, A:F.179, A:F.179, A:Y.354, A:W.356, A:L.360, A:L.360, A:V.416 Hydrogen bonds: A:T.181, A:T.181, A:N.351, A:Q.423, A:Q.423 Water bridges: A:F.179, A:T.181, A:H.183 Salt bridges: A:H.183, A:H.183 pi-Stacking: A:H.176 Metal complexes: A:H.357, H2O.14 HEM.14: 19 residues within 4Å: Chain B: Y.117, A.168, F.169, A.171, 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, V.416, A.419 19 PLIP interactions: 18 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:F.169, B:A.171, B:Q.172, B:F.179, B:V.264, B:Y.354, B:W.356, B:L.360, B:L.360, B:V.416 Hydrogen bonds: B:Y.117, B:T.181, B:N.351, B:Q.423 Water bridges: B:F.179 Salt bridges: B:H.183 pi-Stacking: B:H.176 Metal complexes: B:H.357, H2O.36

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.16: 4 residues within 4Å: Chain B: F.174, F.350, Y.354, S.499 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duggan, K.C. et al., Molecular basis for cyclooxygenase inhibition by the non-steroidal anti-inflammatory drug naproxen. J.Biol.Chem. (2010)

Release Date

2010-09-01

Peptides

Prostaglandin-endoperoxide synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin-endoperoxide synthase 2

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