SMTL ID : 4z0l.1 (1 other biounit)

The murine cyclooxygenase-2 complexed with a nido-dicarbaborate-containing indomethacin derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 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 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.185 Hydrogen bonds: A:R.185 NAG-NAG.2: 7 residues within 4Å: Chain A: L.207, D.208 Chain B: E.109, N.113, Y.116, R.185, F.189 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.189 Hydrogen bonds: B:R.185, A:D.208, A:D.208

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

HEM.3: 18 residues within 4Å: Chain A: A.168, F.169, 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, V.416, A.419 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.169, A:A.171, A:Q.172, A:Q.172, A:F.179, A:V.264, A:W.356, A:L.360, A:L.360, A:V.416, A:V.416 Hydrogen bonds: A:Y.117, A:T.181, A:T.181, A:N.351, A:Q.423 Water bridges: A:F.179 Salt bridges: A:H.183 pi-Stacking: A:H.176 Metal complexes: A:H.357 HEM.9: 19 residues within 4Å: Chain B: Y.117, A.168, 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, V.416, Q.423 19 PLIP interactions: 18 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:A.171, B:Q.172, B:Q.172, B:F.179, B:V.264, B:Y.354, B:W.356, B:L.360, B:L.360, B:V.416 Hydrogen bonds: B:Y.117, B:T.181, B:N.351, B:Q.423 Salt bridges: B:H.183 pi-Stacking: B:H.176 pi-Cation interactions: B:H.357 Metal complexes: B:H.357, H2O.7

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

NAG.4: 5 residues within 4Å: Chain A: S.6, P.8, Y.23, E.35, N.36 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.8 Hydrogen bonds: A:E.35 Water bridges: A:N.36 NAG.5: 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.10: 5 residues within 4Å: Chain B: S.6, P.8, Y.23, E.35, N.36 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.8 Hydrogen bonds: B:Y.23, B:E.35 NAG.11: 4 residues within 4Å: Chain B: Q.375, N.379, S.381, I.382 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.379, B:N.379

2 x 4LA: (R)-7-{[5-methoxy-2-methyl-3-(methoxycarbonylmethyl)-1H-indolyl]carbonyl}-7,8-dicarba-nido-dodeca-hydroundecaborate(Non-covalent)

4LA.6: 17 residues within 4Å: Chain A: H.58, M.82, V.85, L.86, R.89, V.318, L.321, S.322, Y.324, Y.354, W.356, V.492, G.495, A.496, S.499, L.500 Ligands: N1B.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.318 Hydrogen bonds: A:R.89 4LA.12: 18 residues within 4Å: Chain B: H.58, M.82, V.85, L.86, 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 Ligands: N1B.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.321, B:Y.324, B:Y.324 Hydrogen bonds: B:R.89

2 x N1B: (S)-7-{[5-methoxy-2-methyl-3-(methoxycarbonylmethyl)-1H-indolyl]carbonyl}-7,8-dicarba-nido-dodeca-hydroundecaborate(Non-covalent)

N1B.7: 18 residues within 4Å: Chain A: H.58, M.82, V.85, L.86, R.89, V.318, L.321, S.322, Y.324, L.328, Y.354, W.356, V.492, G.495, A.496, S.499, L.500 Ligands: 4LA.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.318 Hydrogen bonds: A:R.89 N1B.13: 18 residues within 4Å: Chain B: H.58, M.82, V.85, L.86, 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 Ligands: 4LA.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.321, B:Y.324, B:Y.324 Hydrogen bonds: B:R.89

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

BOG.8: 7 residues within 4Å: Chain A: E.148, K.149, R.153, R.154, R.407, E.455, E.459 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.148 Hydrogen bonds: A:K.149, A:K.149, A:R.154, A:R.407, A:E.455, A:E.459, A:E.459 Salt bridges: A:K.149, A:R.154, A:R.407 BOG.14: 4 residues within 4Å: Chain B: N.55, T.56, Y.59, P.483 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.56, B:Y.59 Hydrogen bonds: B:N.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neumann, W. et al., nido-Dicarbaborate Induces Potent and Selective Inhibition of Cyclooxygenase-2. Chemmedchem (2016)

Release Date

2015-06-10

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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