SMTL ID : 5ikv.1

The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 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 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Water bridges: B:R.210, B:A.207, B:R.210 Hydrophobic interactions: A:F.188 Hydrogen bonds: A:R.184, A:R.184, 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 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.210, A:R.210, B:R.184, B:R.184 Water bridges: A:A.207 Hydrophobic interactions: B:R.184, B:F.188

2 x FLF: 2-[[3-(TRIFLUOROMETHYL)PHENYL]AMINO] BENZOIC ACID(Non-covalent)

FLF.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:Y.323, A:Y.353, A:W.355, A:V.491, A:A.495 Hydrogen bonds: A:Y.353, A:Y.353, A:S.498 FLF.12: 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 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.317, B:L.320, B:L.352, B:Y.353, B:W.355, B:V.491, B:A.495 Hydrogen bonds: B:Y.353, B:Y.353, B:S.498

2 x COH: PROTOPORPHYRIN IX CONTAINING CO(Non-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 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:F.168, A:A.170, A:Q.171, A:F.178, A:V.263, A:Y.353, A:W.355, A:L.358, A:L.359, A:I.376, A:V.415 Hydrogen bonds: A:Y.116, A:T.180, A:N.350, A:N.350, A:Q.422 Water bridges: A:H.182, A:H.182 Salt bridges: A:H.182 pi-Stacking: A:H.175, A:H.354 Metal complexes: A:H.356 COH.13: 27 residues within 4Å: Chain B: 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 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:F.168, B:Q.171, B:F.178, B:Y.353, B:W.355, B:L.359, B:V.415, B:V.415 Hydrogen bonds: B:T.180, B:N.350, B:N.350, B:Q.422 Salt bridges: B:H.182, B:H.182 pi-Stacking: B:H.175 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:E.384, A:E.384 NAG.14: 6 residues within 4Å: Chain B: Y.370, Q.374, N.378, S.380, I.381, E.384 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.380

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

NH4.6: 5 residues within 4Å: Chain A: R.208, K.211, Q.238, A.239, E.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.208, A:K.211 NH4.7: 4 residues within 4Å: Chain A: N.371, Y.372, Q.373, A.411 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.372 NH4.8: 4 residues within 4Å: Chain A: P.159, R.401, P.482, D.483 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.401, A:R.401, A:D.483, A:D.483, A:D.483 NH4.9: 2 residues within 4Å: Chain A: E.40, F.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.41 NH4.10: 6 residues within 4Å: Chain A: R.11, V.13, D.93, Y.98, K.105 Chain B: K.514 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.11, A:Y.98, A:Y.98, A:K.105 NH4.15: 4 residues within 4Å: Chain B: R.208, K.211, A.239, E.240 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.208, B:K.211 Water bridges: B:T.205 NH4.16: 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 NH4.17: 2 residues within 4Å: Chain B: R.401, D.483 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.401, B:R.401, B:D.483, B:D.483 NH4.18: 6 residues within 4Å: Chain A: K.514 Chain B: R.11, V.13, D.93, Y.98, K.105 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.11, B:R.11, B:Y.98, B:K.105 Water bridges: B:R.11

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

BOG.11: 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:I.526, A:A.530, A:N.538 Hydrogen bonds: A:N.538

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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