SMTL ID : 3ntg.2 (1 other biounit)

Crystal structure of COX-2 with selective compound 23d-(R)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 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: 6 residues within 4Å: Chain A: E.109, N.113, Y.116, R.185, F.189 Chain B: D.208 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.208, B:D.208, A:R.185 Water bridges: B:L.207 NAG-NAG.2: 6 residues within 4Å: Chain A: L.207 Chain B: E.109, N.113, Y.116, R.185, F.189 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.185 Hydrogen bonds: B:R.185 Water bridges: A:L.207

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

HEM.3: 22 residues within 4Å: Chain A: Y.117, A.168, F.169, A.171, Q.172, T.175, 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.413, V.416, Q.423 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.169, A:Q.172, A:F.179, A:F.179, A:V.264, A:Y.354, A:W.356, A:L.360, A:L.360, A:L.377, A:V.413, A:V.416 Hydrogen bonds: A:Y.117, A:T.181, A:T.181, A:N.351 Salt bridges: A:H.183 pi-Stacking: A:H.176, A:H.355 Metal complexes: A:H.357, H2O.2 HEM.6: 21 residues within 4Å: Chain B: Y.117, A.168, F.169, A.171, Q.172, T.175, H.176, F.179, K.180, T.181, H.183, L.263, V.264, N.351, Y.354, H.355, W.356, H.357, L.360, L.377, V.416 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:F.169, B:A.171, B:Q.172, B:F.179, B:L.263, B:V.264, B:Y.354, B:W.356, B:L.360, B:L.377, B:V.416 Hydrogen bonds: B:Y.117, B:T.181, B:N.351 Salt bridges: B:H.183 pi-Stacking: B:H.176 Metal complexes: B:H.357

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

NAG.4: 5 residues within 4Å: Chain A: Y.371, K.374, Q.375, N.379, I.382 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.371, A:Y.371, A:N.379 NAG.7: 5 residues within 4Å: Chain B: K.374, Q.375, N.379, S.381, I.382 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.379 Water bridges: B:E.385

2 x D72: (2R)-6,8-dichloro-7-(2-methylpropoxy)-2-(trifluoromethyl)-2H-chromene-3-carboxylic acid(Non-covalent)

D72.5: 14 residues within 4Å: Chain A: M.82, V.85, R.89, V.318, S.322, Y.324, L.328, W.356, M.491, V.492, G.495, A.496, S.499, L.500 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.324, A:W.356, A:V.492, A:A.496 Hydrogen bonds: A:Y.324 Salt bridges: A:R.89 Halogen bonds: A:S.499 D72.9: 15 residues within 4Å: Chain B: V.85, R.89, V.318, L.321, S.322, Y.324, L.328, Y.354, W.356, F.487, V.492, G.495, A.496, S.499, L.500 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.324, B:Y.354, B:W.356, B:W.356, B:F.487, B:V.492, B:A.496 Salt bridges: B:R.89

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

BOG.8: 6 residues within 4Å: Chain B: E.148, L.152, R.153, R.154, I.411, Q.414 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.144, B:Q.414

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J.L. et al., The novel benzopyran class of selective cyclooxygenase-2 inhibitors. Part 2: The second clinical candidate having a shorter and favorable human half-life. Bioorg.Med.Chem.Lett. (2010)

Release Date

2010-10-27

Peptides

Prostaglandin G/H synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Prostaglandin G/H synthase 2

Related Entries With Identical Sequence