SMTL ID : 4ph9.1

The structure of Ibuprofen bound to cyclooxygenase-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

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.1: 7 residues within 4Å: Chain A: E.109, N.113, Y.116, R.185, F.189 Chain B: L.207, D.208 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.208, A:R.185 Water bridges: B:L.207 NAG-NAG.2: 5 residues within 4Å: Chain B: S.6, P.8, Y.23, E.35, N.36 No protein-ligand interaction detected (PLIP)

1 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.3: 7 residues within 4Å: Chain A: L.207, D.208 Chain B: E.109, N.113, Y.116, R.185, F.189 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.185, A:D.208 Water bridges: A:D.208

2 x IBP: IBUPROFEN(Non-covalent)

IBP.4: 12 residues within 4Å: Chain A: V.85, R.89, V.318, Y.324, L.328, W.356, M.491, V.492, G.495, A.496, S.499, L.500 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.318, A:Y.324, A:L.328, A:W.356, A:A.496 Salt bridges: A:R.89 IBP.18: 14 residues within 4Å: Chain B: V.85, R.89, V.318, Y.324, L.328, Y.354, W.356, M.491, V.492, G.495, A.496, S.499, L.500 Ligands: EDO.30 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.318, B:Y.324, B:L.328, B:Y.354, B:W.356, B:A.496 Hydrogen bonds: B:Y.324, B:Y.324 Salt bridges: B:R.89

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

HEM.5: 20 residues within 4Å: Chain A: Y.117, A.168, A.171, Q.172, H.176, F.179, K.180, T.181, H.183, N.351, Y.354, H.355, W.356, H.357, L.360, F.364, L.377, V.416, A.419, Q.423 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:A.171, A:Q.172, A:Q.172, A:F.179, A:Y.354, A:W.356, A:L.360, A:F.364, A:L.377, A:V.416 Hydrogen bonds: A:Y.117, A:F.179, A:T.181, A:N.351, A:Q.423 Water bridges: A:T.181 Salt bridges: A:H.183 pi-Stacking: A:H.176 Metal complexes: A:H.357, H2O.5 HEM.19: 20 residues within 4Å: Chain B: Y.117, A.168, A.171, Q.172, H.176, F.179, K.180, T.181, H.183, V.264, N.351, Y.354, H.355, W.356, H.357, L.360, L.377, V.416, A.419, Q.423 18 PLIP interactions: 17 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:A.171, B:Q.172, B:F.179, B:V.264, B:Y.354, B:W.356, B:L.360, B:L.377, B:V.416 Hydrogen bonds: B:T.181, B:T.181, B:N.351, B:Q.423 Water bridges: B:F.179 Salt bridges: B:H.183 pi-Stacking: B:H.176 Metal complexes: B:H.357, H2O.26

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

BOG.6: 6 residues within 4Å: Chain A: E.148, L.152, R.153, R.154, I.411, Q.414 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.152, A:R.154, A:I.411 Hydrogen bonds: A:K.144, A:Q.414 BOG.7: 11 residues within 4Å: Chain A: K.51, P.52, T.53, P.54, V.57, W.68, Y.84, V.85, S.88, R.89, E.493 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.57, A:W.68, A:Y.84, A:V.85 Hydrogen bonds: A:K.51, A:K.51, A:P.52, A:S.88, A:S.88, A:S.88 Water bridges: A:R.89, A:R.89 Salt bridges: A:R.89 BOG.20: 12 residues within 4Å: Chain B: K.51, P.52, T.53, P.54, V.57, I.60, L.61, Y.84, S.88, R.89, L.92, E.493 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.60, B:L.61, B:Y.84, B:Y.84 Hydrogen bonds: B:K.51, B:K.51, B:P.52, B:S.88, B:S.88, B:R.89 Water bridges: B:S.88, B:S.88, B:R.89, B:S.440 Salt bridges: B:R.89

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

NAG.8: 4 residues within 4Å: Chain A: P.8, Y.23, E.35, N.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.23 Water bridges: A:N.36 NAG.9: 4 residues within 4Å: Chain A: Q.375, N.379, S.381, I.382 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.379 NAG.21: 5 residues within 4Å: Chain B: Q.375, N.379, S.381, I.382, E.385 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.379, B:E.385, B:E.385

4 x AKR: ACRYLIC ACID(Non-covalent)

AKR.10: 4 residues within 4Å: Chain A: S.446, F.447, E.448, K.461 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.447, A:E.448 Hydrogen bonds: A:F.447 Water bridges: A:K.461 Salt bridges: A:K.461 AKR.11: 6 residues within 4Å: Chain A: T.206, R.209, K.212, Q.239, V.240, E.241 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.209 Hydrogen bonds: A:E.241 Salt bridges: A:R.209, A:K.212 AKR.22: 6 residues within 4Å: Chain B: D.208, R.209, K.212, Q.239, V.240, E.241 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:D.208, B:R.209, B:K.212 Hydrogen bonds: B:Q.239, B:E.241 Salt bridges: B:R.209, B:K.212 AKR.23: 4 residues within 4Å: Chain B: S.446, F.447, E.448, K.461 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.447, B:K.461 Hydrogen bonds: B:F.447, B:E.448 Water bridges: B:E.448

13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 7 residues within 4Å: Chain A: P.131, M.132, L.140, S.424, R.425, K.428, Y.429 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.428 Water bridges: A:E.471, A:E.471 EDO.13: 8 residues within 4Å: Chain A: E.277, R.280, E.308, A.531, S.535, L.536, N.539, N.540 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.280, A:S.535, A:N.539, A:N.540 Water bridges: A:T.530, A:T.530, A:T.530 EDO.14: 6 residues within 4Å: Chain A: P.516, S.517, G.521, E.522 Chain B: M.16, K.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.522 EDO.15: 4 residues within 4Å: Chain A: K.220, Y.223, V.230, N.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.220, A:K.220, A:N.279 EDO.16: 4 residues within 4Å: Chain A: S.112, L.114 Chain B: L.114, L.193 No protein-ligand interaction detected (PLIP) EDO.17: 8 residues within 4Å: Chain A: F.178, V.197, N.344, I.346, F.498, S.499, G.502, L.503 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.344, A:S.499 EDO.24: 7 residues within 4Å: Chain B: P.131, M.132, L.140, S.424, R.425, K.428, Y.429 No protein-ligand interaction detected (PLIP) EDO.25: 8 residues within 4Å: Chain B: E.277, R.280, E.308, A.531, S.535, L.536, N.539, N.540 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.280, B:N.539, B:N.540 Water bridges: B:T.530, B:T.530, B:S.535 EDO.26: 4 residues within 4Å: Chain A: L.114, L.193 Chain B: S.112, L.114 No protein-ligand interaction detected (PLIP) EDO.27: 4 residues within 4Å: Chain A: P.511 Chain B: Q.339, F.340, Q.341 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.341 Water bridges: B:S.95, A:F.340, A:F.340 EDO.28: 8 residues within 4Å: Chain B: F.178, V.197, N.344, I.346, S.499, G.502, L.503 Ligands: EDO.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.344, B:S.499 Water bridges: B:G.502 EDO.29: 4 residues within 4Å: Chain B: C.538, N.539, V.541, C.544 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.541, B:G.543, B:C.544 EDO.30: 9 residues within 4Å: Chain B: F.174, V.313, Y.317, F.350, Y.354, S.499, L.503 Ligands: IBP.18, EDO.28 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.354, B:S.499, B:S.499

Links

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Citation

Orlando, B.J. et al., The structure of ibuprofen bound to cyclooxygenase-2. J.Struct.Biol. (2015)

Release Date

2014-11-26

Peptides

Prostaglandin G/H synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin G/H synthase 2