SMTL ID : 5ikt.1

The Structure of Tolfenamic Acid Bound to Human Cyclooxygenase-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 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 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.188 Hydrogen bonds: A:R.184, A:R.184, B:R.210 NAG-NAG-MAN.3: 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 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.210, A:R.210, B:R.184 Water bridges: A:R.210

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

NAG-NAG.2: 7 residues within 4Å: Chain A: Y.370, Q.373, Q.374, N.378, S.380, I.381, E.384 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 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 Hydrophobic interactions: B:E.384

2 x TLF: 2-[(3-chloro-2-methylphenyl)amino]benzoic acid(Non-covalent)

TLF.5: 17 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, M.490, V.491, G.494, A.495, S.498, L.499 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.317, A:L.320, A:Y.323, A:L.352, A:Y.353, A:W.355, A:V.491, A:A.495, A:L.499 Hydrogen bonds: A:Y.353, A:Y.353, A:S.498 TLF.10: 17 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, M.490, V.491, G.494, A.495, S.498, L.499 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.317, B:L.320, B:Y.323, B:L.352, B:Y.353, B:W.355, B:V.491, B:A.495, B:L.499 Hydrogen bonds: B:Y.353, B:Y.353, B:S.498

2 x COH: PROTOPORPHYRIN IX CONTAINING CO(Covalent)

COH.6: 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 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:Q.171, A:F.178, A:F.178, A:V.263, A:Y.353, A:L.359, A:F.363, A:I.376, A:V.415 Hydrogen bonds: A:Y.116, A:T.180, A:N.350, A:Q.422 Water bridges: A:F.178 Salt bridges: A:H.182, A:H.182 pi-Stacking: A:H.175, A:H.354 Metal complexes: A:H.356 COH.11: 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 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:Q.171, B:F.178, B:F.178, B:V.263, B:Y.353, B:L.359, B:L.359, B:F.363, B:V.415 Hydrogen bonds: B:Y.116, B:T.180, B:T.180, B:N.350, B:Q.422 Water bridges: B:F.178, B:H.354, B:Q.422 Salt bridges: B:H.182, B:H.182 pi-Stacking: B:H.175, B:H.354 Metal complexes: B:H.356

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 5 residues within 4Å: Chain A: R.208, K.211, Q.238, A.239, E.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.240, A:E.258 Salt bridges: A:R.208, A:K.211 PO4.8: 7 residues within 4Å: Chain A: R.11, V.13, D.93, T.97, Y.98, K.105 Chain B: K.514 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.98 Water bridges: A:R.11, B:K.514 Salt bridges: A:R.11, A:K.105, B:K.514 PO4.9: 5 residues within 4Å: Chain A: P.159, R.401, R.481, P.482, D.483 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.483, A:D.483 Salt bridges: A:R.401 PO4.13: 5 residues within 4Å: Chain B: A.207, R.208, K.211, A.239, E.240 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.240 Salt bridges: B:R.208, B:K.211 PO4.14: 7 residues within 4Å: Chain A: K.514 Chain B: R.11, V.13, D.93, T.97, Y.98, K.105 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.98, B:Y.98, B:Y.98 Water bridges: B:R.11, B:R.11, B:R.11, B:R.11, B:R.437 Salt bridges: B:R.11, B:K.105 PO4.15: 6 residues within 4Å: Chain B: P.159, R.401, P.480, R.481, P.482, D.483 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.483, B:D.483, B:D.483 Salt bridges: B:R.401

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

NAG.12: 6 residues within 4Å: Chain B: S.5, P.7, Y.22, E.34, N.35, S.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.34, B:N.35

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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