SMTL ID : 5ikr.1

The Structure of Mefenamic Acid Bound to Human Cyclooxygenase-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-MAN.1: 10 residues within 4Å: Chain A: E.108, N.112, S.114, Y.115, R.184, F.188 Chain B: T.205, L.206, A.207, R.210 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.210, B:R.210 Water bridges: B:A.207, B:R.210 NAG-NAG-MAN.2: 10 residues within 4Å: Chain A: T.205, L.206, A.207, R.210 Chain B: E.108, N.112, S.114, Y.115, R.184, F.188 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.210, A:R.210, A:A.207 Hydrogen bonds: A:R.210

2 x ID8: 2-[(2,3-DIMETHYLPHENYL)AMINO]BENZOIC ACID(Non-covalent)

ID8.3: 18 residues within 4Å: Chain A: V.84, R.88, Y.316, V.317, L.320, S.321, Y.323, L.327, F.349, L.352, Y.353, W.355, M.490, V.491, G.494, A.495, S.498, L.499 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.317, A:L.320, A:Y.353, A:W.355, A:V.491, A:A.495, A:L.499 Hydrogen bonds: A:Y.353, A:S.498 ID8.13: 18 residues within 4Å: Chain B: V.84, R.88, Y.316, V.317, L.320, S.321, Y.323, L.327, F.349, L.352, Y.353, W.355, M.490, V.491, G.494, A.495, S.498, L.499 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.317, B:L.320, B:L.352, B:Y.353, B:W.355, B:W.355, B:V.491, B:A.495, B:L.499 Hydrogen bonds: B:Y.353, B:S.498

2 x COH: PROTOPORPHYRIN IX CONTAINING CO(Covalent)

COH.4: 28 residues within 4Å: Chain A: Y.116, A.167, F.168, A.170, Q.171, T.174, H.175, F.178, K.179, T.180, H.182, L.262, V.263, N.350, Y.353, H.354, W.355, H.356, L.358, L.359, F.363, Y.372, F.375, I.376, V.412, V.415, A.418, Q.422 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:F.168, A:A.170, A:Q.171, A:F.178, A:F.178, A:W.355, A:L.358, A:L.359, A:L.359, A:I.376, A:V.415 Hydrogen bonds: A:Y.116, A:F.178, A:T.180, A:N.350, A:Q.422 Salt bridges: A:H.182, A:H.182 pi-Stacking: A:H.175, A:H.354 Metal complexes: A:H.356 COH.14: 28 residues within 4Å: Chain B: Y.116, A.167, F.168, A.170, Q.171, T.174, H.175, F.178, K.179, T.180, H.182, L.262, V.263, N.350, Y.353, H.354, W.355, H.356, L.358, L.359, F.363, Y.372, F.375, I.376, V.412, V.415, A.418, Q.422 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:F.168, B:A.170, B:Q.171, B:Q.171, B:F.178, B:F.178, B:V.263, B:W.355, B:L.358, B:L.359, B:L.359, B:I.376, B:V.412, B:V.415 Hydrogen bonds: B:Y.116, B:T.180, B:T.180, B:N.350, B:Q.422 Salt bridges: B:H.182, B:H.182 pi-Stacking: B:H.175, B:H.354 Metal complexes: B:H.356

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

NAG.5: 7 residues within 4Å: Chain A: Y.370, Q.373, Q.374, N.378, S.380, I.381, E.384 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.378, A:E.384 NAG.15: 7 residues within 4Å: Chain B: Y.370, Q.373, Q.374, N.378, S.380, I.381, E.384 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.378, B:S.380

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

BOG.6: 6 residues within 4Å: Chain A: L.49, P.51, T.52, T.55, I.59 Ligands: BOG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.52, A:T.52 BOG.7: 9 residues within 4Å: Chain A: T.52, N.54, T.55, Y.58, I.59, F.63, P.482 Ligands: BOG.6, NH4.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.58, A:F.63 Hydrogen bonds: A:N.54, A:T.55 BOG.8: 13 residues within 4Å: Chain A: E.276, R.279, E.307, I.311, Q.525, I.526, T.529, A.530, S.531, S.534, L.535, N.538, N.539 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.535, A:N.538 Hydrogen bonds: A:R.279, A:N.538 BOG.12: 13 residues within 4Å: Chain B: E.276, R.279, E.307, I.311, Q.525, I.526, T.529, A.530, S.531, S.534, L.535, N.538, N.539 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.526, B:A.530, B:L.535, B:N.538 Hydrogen bonds: B:Q.525

5 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.9: 4 residues within 4Å: Chain A: R.208, K.211, A.239, E.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.208, A:K.211 NH4.10: 4 residues within 4Å: Chain A: N.371, Y.372, Q.373, A.411 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.372, A:Q.373 NH4.11: 3 residues within 4Å: Chain A: T.52, N.54 Ligands: BOG.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.52, A:N.54 Water bridges: A:N.54 NH4.16: 4 residues within 4Å: Chain B: R.208, K.211, A.239, E.240 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.208, B:K.211 NH4.17: 4 residues within 4Å: Chain B: N.371, Y.372, Q.373, A.411 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.371, B:Y.372

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Orlando, B.J. et al., Substrate-selective Inhibition of Cyclooxygeanse-2 by Fenamic Acid Derivatives Is Dependent on Peroxide Tone. J.Biol.Chem. (2016)

Release Date

2016-05-25

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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