SMTL ID : 6v3r.2 (1 other biounit)

Crystal structure of murine cycloxygenase in complex with a harmaline analog, 4,9-dihydro-3H-pyrido[3,4-b]indole

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.66 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: 3 interactions with chain A Hydrophobic interactions: A:R.185, A:F.189 Hydrogen bonds: A:R.185 NAG-NAG.2: 5 residues within 4Å: Chain A: L.207 Chain B: E.109, N.113, Y.116, R.185 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.185

2 x Y8A: 9-[(4-chlorophenyl)methyl]-6-methoxy-1-methyl-4,9-dihydro-3H-beta-carboline(Non-covalent)

Y8A.3: 16 residues within 4Å: Chain A: V.85, L.86, R.89, V.318, L.321, S.322, Y.324, L.353, Y.354, 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:V.318, A:L.321, A:Y.354, A:W.356, A:A.496 Y8A.7: 16 residues within 4Å: Chain B: L.86, R.89, V.318, L.321, S.322, Y.324, F.350, L.353, Y.354, W.356, M.491, V.492, G.495, A.496, S.499, L.500 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.321, B:Y.354, B:W.356, B:V.492, B:A.496

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

HEM.4: 18 residues within 4Å: Chain A: A.168, F.169, 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, Q.423 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:F.169, A:Q.172, A:F.179, A:V.264, A:Y.354, A:W.356, A:L.360, A:L.377, A:V.416 Hydrogen bonds: A:Y.117, A:T.181, A:N.351, A:Q.423 Salt bridges: A:H.183 pi-Stacking: A:H.176 Metal complexes: A:H.357 HEM.8: 20 residues within 4Å: Chain B: Y.117, A.168, F.169, 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: 18 interactions with chain B, Hydrophobic interactions: B:F.169, B:Q.172, 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 Salt bridges: B:H.183 pi-Stacking: B:H.176, B:H.355 Metal complexes: B:H.357

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

NAG.5: 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:Y.23, A:Y.23 NAG.6: 5 residues within 4Å: Chain A: K.374, Q.375, N.379, S.381, I.382 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.379 NAG.9: 5 residues within 4Å: Chain B: S.6, P.8, Y.23, E.35, N.36 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.8 Water bridges: B:E.35 NAG.10: 5 residues within 4Å: Chain B: Q.375, N.379, S.381, I.382, E.385 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.379, B:N.379

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

BOG.11: 8 residues within 4Å: Chain B: E.148, K.149, L.152, R.153, R.154, R.407, E.455, E.459 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.152 Hydrogen bonds: B:K.149, B:K.149, B:R.154, B:R.407, B:R.407, B:E.455, B:E.455, B:E.459 Salt bridges: B:K.149, B:R.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Uddin, M.J. et al., Harmaline Analogs as Substrate-Selective Cyclooxygenase-2 Inhibitors. Acs Med.Chem.Lett. (2020)

Release Date

2020-02-26

Peptides

Prostaglandin G/H synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Prostaglandin G/H synthase 2

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