SMTL ID : 5ikq.1

The Structure of Meclofenamic Acid Bound to Human Cyclooxygenase-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.1: 11 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, K.211 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.211, A:R.184, B:R.210 Hydrophobic interactions: A:F.188 NAG-NAG-MAN-MAN.2: 11 residues within 4Å: Chain A: T.205, L.206, A.207, R.210, K.211 Chain B: E.108, N.112, S.114, Y.115, R.184, F.188 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.210, B:R.184, B:R.184

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

BOG.3: 9 residues within 4Å: Chain A: E.147, K.148, L.151, R.152, R.153, R.406, P.410, E.454, E.458 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.148, A:R.153, A:R.153, A:R.406, A:R.406, A:E.454, A:E.454, A:E.458, A:E.458 Salt bridges: A:R.153

2 x JMS: 2-[(2,6-dichloro-3-methyl-phenyl)amino]benzoic acid(Non-covalent)

JMS.4: 18 residues within 4Å: Chain A: V.84, R.88, Y.316, V.317, L.320, S.321, Y.323, F.349, L.352, Y.353, W.355, F.486, M.490, V.491, G.494, A.495, S.498, L.499 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.84, A:V.317, A:Y.323, A:Y.353, A:W.355, A:V.491, A:A.495, A:L.499 Hydrogen bonds: A:Y.353, A:S.498 JMS.10: 18 residues within 4Å: Chain B: V.84, R.88, Y.316, V.317, L.320, S.321, Y.323, F.349, L.352, Y.353, W.355, F.486, M.490, V.491, G.494, A.495, S.498, L.499 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.317, B:L.320, B:Y.353, B:W.355, B:V.491, B:A.495 Hydrogen bonds: B:Y.353, B:S.498

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

NAG.5: 6 residues within 4Å: Chain A: S.5, P.7, Q.9, Y.22, E.34, N.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.5, A:Y.22, A:E.34 NAG.6: 8 residues within 4Å: Chain A: Y.370, Q.373, Q.374, F.375, I.376, N.378, I.381, E.384 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.384 NAG.11: 5 residues within 4Å: Chain B: S.5, P.7, Y.22, E.34, N.35 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.5, B:E.34, B:E.34 NAG.12: 7 residues within 4Å: Chain B: Y.370, Q.373, Q.374, N.378, S.380, I.381, E.384 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.380, B:E.384 Water bridges: B:N.378, B:N.378

2 x COH: PROTOPORPHYRIN IX CONTAINING CO(Covalent)

COH.7: 27 residues within 4Å: Chain A: Y.116, A.167, F.168, A.170, Q.171, 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 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:A.170, A:Q.171, A:F.178, A:F.178, A:W.355, A:L.358, A:L.359, A:V.415 Hydrogen bonds: A:Y.116, A:T.180, A:N.350, A:Q.422 Salt bridges: A:H.182, A:H.182 pi-Stacking: A:H.175 COH.9: 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 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:A.170, B:F.178, B:W.355, B:W.355, B:L.358, B:L.359, B:I.376, B:V.415 Hydrogen bonds: B:Y.116, B:F.178, 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

3 x AKR: ACRYLIC ACID(Non-covalent)

AKR.8: 7 residues within 4Å: Chain A: T.205, R.208, K.211, Q.238, A.239, E.240, E.258 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.208 Hydrogen bonds: A:E.240 Water bridges: A:E.240 Salt bridges: A:R.208, A:K.211 AKR.13: 5 residues within 4Å: Chain B: R.208, K.211, Q.238, A.239, E.240 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.240 Salt bridges: B:R.208, B:K.211 AKR.14: 4 residues within 4Å: Chain B: N.371, Y.372, Q.373, A.411 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.411 Hydrogen bonds: B:Y.372, B:Q.373

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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