SMTL ID : 3ntb.1 (1 other biounit)

Structure of 6-methylthio naproxen analog bound to mCOX-2.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-NAG.1: 7 residues within 4Å: Chain A: E.109, N.113, Y.116, R.185, F.189 Chain B: L.207, D.208 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.2: 7 residues within 4Å: Chain A: L.207, D.208 Chain B: E.109, N.113, Y.116, R.185, F.189 No protein-ligand interaction detected (PLIP)

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

HEM.3: 19 residues within 4Å: Chain A: A.168, F.169, A.171, Q.172, T.175, 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 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.169, A:A.171, 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:T.181, A:T.181, A:N.351 Water bridges: A:Q.423 Salt bridges: A:H.183 pi-Stacking: A:H.176, A:H.355 Metal complexes: A:H.357 HEM.9: 21 residues within 4Å: Chain B: Y.117, A.168, F.169, A.171, Q.172, T.175, 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 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:F.169, B:A.171, B:Q.172, B:Q.172, B:F.179, B:V.264, B:Y.354, B:W.356, B:L.360, B:L.377, B:V.416 Hydrogen bonds: B:T.181, B:N.351 Water bridges: B:F.179, B:H.183 Salt bridges: B:H.183 pi-Stacking: B:H.176, B:H.355 Metal complexes: B:H.357, H2O.11

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

NAG.4: 4 residues within 4Å: Chain A: P.8, Y.23, E.35, N.36 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.8 NAG.5: 4 residues within 4Å: Chain A: Q.375, N.379, S.381, I.382 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.379 NAG.10: 5 residues within 4Å: Chain B: S.6, P.8, Y.23, E.35, N.36 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.8 Hydrogen bonds: B:Y.23, B:Y.23, B:N.36 NAG.11: 5 residues within 4Å: Chain B: Y.371, Q.375, Y.378, N.379, I.382 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.378 Hydrogen bonds: B:Y.371, B:N.379

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

BOG.6: 6 residues within 4Å: Chain A: E.148, L.152, R.153, R.154, I.411, Q.414 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.152 Hydrogen bonds: A:Q.414 BOG.8: 10 residues within 4Å: Chain A: K.51, P.52, P.54, V.57, Y.84, V.85, S.88, R.89, L.92, E.493 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.84, A:V.85 Hydrogen bonds: A:K.51, A:P.52, A:S.88, A:S.88, A:S.88, A:R.89, A:E.493 Salt bridges: A:R.89 BOG.13: 15 residues within 4Å: Chain B: K.51, P.52, P.54, V.57, I.60, L.61, W.68, Y.84, V.85, S.88, R.89, Y.91, L.92, S.440, E.493 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.60, B:L.61, B:W.68, B:Y.84, B:V.85 Hydrogen bonds: B:K.51, B:P.52, B:S.88, B:S.88, B:S.88, B:R.89 Salt bridges: B:R.89

2 x T1N: (2S)-2-[6-(methylsulfanyl)naphthalen-2-yl]propanoic acid(Non-covalent)

T1N.7: 12 residues within 4Å: Chain A: R.89, V.318, L.321, Y.324, L.328, F.350, Y.354, W.356, V.492, G.495, A.496, 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 T1N.12: 11 residues within 4Å: Chain B: R.89, V.318, Y.324, L.328, F.350, Y.354, W.356, V.492, G.495, A.496, L.500 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.318, B:Y.324, B:L.328, B:V.492, B:A.496 Hydrogen bonds: B:Y.324 Salt bridges: B:R.89

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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