SMTL ID : 7jxt.1

Ovine COX-1 in complex with the subtype-selective derivative 2a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

homo-dimer

Ligands

6 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: P.4, Y.7, P.9, Y.24, P.36, N.37 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: N.113, S.115, Y.116, M.185, F.189 Chain B: L.207, E.208, Y.211 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.185 NAG-NAG.3: 9 residues within 4Å: Chain A: Q.369, Y.371, E.374, Q.375, N.379, S.381, M.382, D.385, Y.386 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.369 NAG-NAG.4: 6 residues within 4Å: Chain B: P.4, Y.7, P.9, Y.24, P.36, N.37 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.7 NAG-NAG.5: 9 residues within 4Å: Chain A: L.207, E.208, Y.211 Chain B: E.109, N.113, S.115, Y.116, M.185, F.189 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:M.185 NAG-NAG.6: 8 residues within 4Å: Chain B: Q.369, Y.371, E.374, Q.375, N.379, M.382, D.385, Y.386 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.369

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

HEM.7: 25 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, L.264, N.351, Y.354, H.355, W.356, H.357, L.359, M.360, F.364, Y.373, L.377, I.413, H.415, V.416, D.419 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:Q.172, A:F.179, A:L.264, A:Y.354, A:W.356, A:L.377, A:I.413, A:V.416 Hydrogen bonds: A:T.181, A:T.181, A:N.351 pi-Stacking: A:H.176 Metal complexes: A:H.357 HEM.9: 25 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, L.264, N.351, Y.354, H.355, W.356, H.357, L.359, M.360, F.364, Y.373, L.377, I.413, H.415, V.416, D.419 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:F.179, B:L.264, B:L.264, B:Y.354, B:W.356, B:V.416 Hydrogen bonds: B:T.181, B:T.181, B:N.351, B:D.419 pi-Stacking: B:H.176 Metal complexes: B:H.357

2 x W8M: 2-[4,5-bis(2-chlorophenyl)-1H-imidazol-2-yl]-6-(prop-2-en-1-yl)phenyl methoxyacetate(Non-covalent)

W8M.8: 25 residues within 4Å: Chain A: M.82, V.85, L.86, R.89, I.314, Y.317, V.318, L.321, S.322, Y.324, L.328, K.329, F.330, L.334, L.353, W.356, F.487, M.491, I.492, G.495, A.496, S.499, L.500, L.503, L.504 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.314, A:I.314, A:V.318, A:L.321, A:Y.324, A:W.356, A:W.356, A:I.492, A:I.492, A:L.500, A:L.500, A:L.503, A:L.504 Hydrogen bonds: A:S.499, A:S.499 Salt bridges: A:R.89 W8M.10: 26 residues within 4Å: Chain B: M.82, V.85, L.86, R.89, V.313, I.314, Y.317, V.318, L.321, S.322, Y.324, L.328, K.329, F.330, L.353, Y.354, W.356, F.487, M.491, I.492, G.495, A.496, S.499, L.500, L.503, L.504 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.86, B:I.314, B:I.314, B:V.318, B:V.318, B:L.321, B:Y.324, B:W.356, B:I.492, B:I.492, B:A.496, B:L.500, B:L.500, B:L.503, B:L.504 Hydrogen bonds: B:S.499, B:S.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Friedrich, L. et al., Learning from Nature: From a Marine Natural Product to Synthetic Cyclooxygenase-1 Inhibitors by Automated De Novo Design. Adv Sci (2021)

Release Date

2021-09-01

Peptides

Prostaglandin G/H synthase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin G/H synthase 1