SMTL ID : 4z0l.2 (1 other biounit)

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

Coordinates

PDB Format Compare

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 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.189 Hydrogen bonds: A:R.185, B:D.208, B:D.208 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 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.185, 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: 19 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, H.357, L.360, V.416, A.419 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:F.169, A:A.171, A:Q.172, A:F.179, A:V.264, A:L.360, A:V.416, A:V.416 Hydrogen bonds: A:Y.117, A:T.181, A:T.181, A:N.351 Water bridges: A:F.179 Salt bridges: A:H.183 pi-Stacking: A:H.176 Metal complexes: A:H.357 HEM.10: 17 residues within 4Å: Chain B: Y.117, 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, H.357, L.360, V.416 16 PLIP interactions: 15 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:F.169, B:A.171, B:Q.172, B:Q.172, B:F.179, B:V.264, B:L.360, B:V.416 Hydrogen bonds: B:Y.117, B:T.181, B:N.351 Water bridges: B:F.179 Salt bridges: B:H.183 pi-Stacking: B:H.176 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 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.8 Hydrogen bonds: A:E.35 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.11: 4 residues within 4Å: Chain B: 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.12: 4 residues within 4Å: Chain B: Q.375, N.379, S.381, I.382 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.379 Water bridges: 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, W.356, R.482, F.487, V.492, G.495, A.496, S.499 Ligands: N1B.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.318, A:L.321, A:V.492 Hydrogen bonds: A:R.89, A:S.499 4LA.13: 19 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, W.356, R.482, M.491, V.492, G.495, A.496, S.499, L.500 Ligands: N1B.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.318, B:V.318 Hydrogen bonds: B:R.89, B:S.499

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

N1B.7: 17 residues within 4Å: Chain A: H.58, M.82, V.85, L.86, R.89, V.318, L.321, S.322, Y.324, W.356, R.482, F.487, V.492, G.495, A.496, S.499 Ligands: 4LA.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.318, A:L.321, A:V.492 Hydrogen bonds: A:R.89, A:S.499 N1B.14: 19 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, W.356, R.482, M.491, V.492, G.495, A.496, S.499, L.500 Ligands: 4LA.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.318, B:V.318 Hydrogen bonds: B:R.89, B:S.499

3 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 10 PLIP interactions: 10 interactions with chain A 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.9: 4 residues within 4Å: Chain A: N.55, T.56, Y.59, P.483 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.56, A:Y.59 Hydrogen bonds: A:N.55 BOG.15: 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
C

B
D

Prostaglandin G/H synthase 2

Related Entries With Identical Sequence