SMTL ID : 2oyu.1

Indomethacin-(S)-alpha-ethyl-ethanolamide bound to Cyclooxygenase-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

4 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: 5 residues within 4Å: Chain A: Y.38, P.40, Y.55, P.67, N.68 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.38 NAG-NAG.3: 5 residues within 4Å: Chain A: Y.402, Q.406, N.410, M.413, Y.417 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.402, A:Q.406 NAG-NAG.8: 5 residues within 4Å: Chain B: Y.38, P.40, Y.55, P.67, N.68 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.38 NAG-NAG.10: 5 residues within 4Å: Chain B: Y.402, Q.406, N.410, M.413, Y.417 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.406

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

NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: E.140, N.144, Y.147, M.216 Chain B: L.238, E.239, Y.242 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.216 Hydrogen bonds: B:E.239 NAG-NAG-BMA.9: 7 residues within 4Å: Chain A: L.238, E.239, Y.242 Chain B: E.140, N.144, Y.147, M.216 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.239, A:E.239 Hydrophobic interactions: B:M.216

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

BOG.4: 3 residues within 4Å: Chain A: S.87, F.88, F.91 No protein-ligand interaction detected (PLIP) BOG.5: 6 residues within 4Å: Chain A: P.86, I.89, V.119, R.120, L.123, E.524 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.524 Salt bridges: A:R.120 BOG.11: 3 residues within 4Å: Chain B: S.87, F.88, F.91 No protein-ligand interaction detected (PLIP) BOG.12: 6 residues within 4Å: Chain B: P.86, I.89, V.119, R.120, L.123, E.524 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.524 Salt bridges: B:R.120

2 x IMS: 2-[1-(4-CHLOROBENZOYL)-5-METHOXY-2-METHYL-1H-INDOL-3-YL]-N-[(1S)-1-(HYDROXYMETHYL)PROPYL]ACETAMIDE(Non-covalent)

IMS.6: 19 residues within 4Å: Chain A: H.90, M.113, V.116, R.120, Q.192, V.349, L.352, S.353, Y.355, L.359, W.387, S.516, I.517, F.518, I.523, G.526, A.527, S.530, L.531 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.116, A:V.349, A:L.352, A:Y.355, A:L.359, A:I.517, A:F.518, A:F.518, A:F.518, A:I.523, A:A.527, A:L.531, A:L.531 Hydrogen bonds: A:H.90, A:L.352, A:Y.355 Water bridges: A:H.90 IMS.13: 19 residues within 4Å: Chain B: H.90, M.113, V.116, R.120, Q.192, V.349, L.352, S.353, Y.355, L.359, W.387, S.516, I.517, F.518, I.523, G.526, A.527, S.530, L.531 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.116, B:V.349, B:L.352, B:Y.355, B:L.359, B:I.517, B:F.518, B:F.518, B:F.518, B:I.523, B:A.527, B:L.531, B:L.531 Hydrogen bonds: B:H.90, B:L.352

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

HEM.7: 21 residues within 4Å: Chain A: A.199, A.202, Q.203, T.206, H.207, F.210, K.211, T.212, L.295, N.382, Y.385, H.386, W.387, H.388, L.390, M.391, L.408, I.444, V.447, D.450, E.454 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:A.202, A:Q.203, A:F.210, A:F.210, A:L.295, A:W.387, A:L.390, A:L.408, A:I.444, A:V.447 Hydrogen bonds: A:T.212, A:N.382, A:N.382 pi-Stacking: A:H.207 Metal complexes: A:H.388 HEM.14: 21 residues within 4Å: Chain B: A.199, A.202, Q.203, T.206, H.207, F.210, K.211, T.212, L.295, N.382, Y.385, H.386, W.387, H.388, L.390, M.391, L.408, I.444, V.447, D.450, E.454 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:A.202, B:Q.203, B:F.210, B:F.210, B:L.295, B:W.387, B:L.390, B:L.408, B:I.444, B:V.447 Hydrogen bonds: B:T.212, B:T.212, B:N.382, B:N.382, B:D.450 pi-Stacking: B:H.207 Metal complexes: B:H.388

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harman, C.A. et al., Structural basis of enantioselective inhibition of cyclooxygenase-1 by S-alpha-substituted indomethacin ethanolamides. J.Biol.Chem. (2007)

Release Date

2007-07-24

Peptides

Prostaglandin G/H synthase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
P

Prostaglandin G/H synthase 1

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