SMTL ID : 5kir.1

The Structure of Vioxx Bound to Human COX-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 9 residues within 4Å: Chain A: E.108, N.112, S.114, Y.115, R.184, F.188 Chain B: L.206, A.207, R.210 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.210 Hydrophobic interactions: A:F.188 NAG-NAG-MAN.2: 10 residues within 4Å: Chain A: T.205, L.206, A.207, R.210 Chain B: E.108, N.112, S.114, Y.115, R.184, F.188 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.188 Hydrogen bonds: B:R.184, B:R.184, A:R.210

2 x RCX: Rofecoxib(Non-covalent)

RCX.3: 17 residues within 4Å: Chain A: H.57, Q.160, V.317, L.320, S.321, Y.323, W.355, R.481, A.484, I.485, F.486, M.490, V.491, G.494, A.495, S.498, L.499 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.317, A:L.320, A:L.320, A:W.355, A:V.491, A:A.495 RCX.11: 17 residues within 4Å: Chain B: H.57, Q.160, V.317, L.320, S.321, Y.323, W.355, R.481, A.484, I.485, F.486, M.490, V.491, G.494, A.495, S.498, L.499 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.317, B:L.320, B:L.320, B:W.355, B:V.491, B:A.495

2 x COH: PROTOPORPHYRIN IX CONTAINING CO(Non-covalent)(Covalent)

COH.4: 28 residues within 4Å: Chain A: Y.116, A.167, F.168, A.170, Q.171, T.174, H.175, F.178, K.179, T.180, H.182, L.262, V.263, N.350, Y.353, H.354, W.355, H.356, L.358, L.359, F.363, Y.372, F.375, I.376, V.412, V.415, A.418, Q.422 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:F.168, A:A.170, A:Q.171, A:F.178, A:V.263, A:Y.353, A:L.359, A:V.415 Hydrogen bonds: A:F.178, A:T.180, A:T.180, A:N.350, A:Q.422 Salt bridges: A:H.182, A:H.182 pi-Stacking: A:H.175 Metal complexes: A:H.356 COH.12: 28 residues within 4Å: Chain B: Y.116, A.167, F.168, A.170, Q.171, T.174, H.175, F.178, K.179, T.180, H.182, L.262, V.263, N.350, Y.353, H.354, W.355, H.356, L.358, L.359, F.363, Y.372, F.375, I.376, V.412, V.415, A.418, Q.422 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:A.170, B:Q.171, B:F.178, B:Y.353, B:L.359, B:V.412, B:V.415 Hydrogen bonds: B:F.178, B:T.180, B:N.350, B:Q.422 Water bridges: B:H.182, B:H.182 Salt bridges: B:H.182 pi-Stacking: B:H.175 Metal complexes: B:H.356

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

NAG.5: 7 residues within 4Å: Chain A: Y.370, Q.373, Q.374, N.378, S.380, I.381, E.384 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.380 NAG.13: 6 residues within 4Å: Chain B: Y.370, Q.374, N.378, S.380, I.381, E.384 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.380

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.6: 3 residues within 4Å: Chain A: R.401, P.482, D.483 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.401, A:D.483, A:D.483, A:D.483 NH4.14: 5 residues within 4Å: Chain B: P.159, R.401, P.482, D.483, A.484 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.401, B:R.401, B:D.483, B:D.483, B:D.483

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: K.50, P.53, Y.83, S.87, R.88, L.91, M.439, E.492 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.492

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 6 residues within 4Å: Chain A: R.11, V.13, D.93, Y.98, K.105 Chain B: K.514 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.11, A:D.93, A:D.93, A:Y.98 Salt bridges: A:R.11, A:K.105 PO4.9: 5 residues within 4Å: Chain A: R.208, K.211, Q.238, A.239, E.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.238, A:E.240 Salt bridges: A:R.208, A:K.211 PO4.10: 3 residues within 4Å: Chain A: H.319, F.548, S.549 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.549 Salt bridges: A:H.319 PO4.15: 7 residues within 4Å: Chain A: K.514 Chain B: R.11, V.13, D.93, T.97, Y.98, K.105 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.93, B:Y.98 Salt bridges: B:R.11, B:K.105, A:K.514 PO4.16: 6 residues within 4Å: Chain B: A.207, R.208, K.211, Q.238, A.239, E.240 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.240 Salt bridges: B:R.208, B:K.211 PO4.17: 4 residues within 4Å: Chain B: H.319, S.547, F.548, S.549 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.549 Salt bridges: B:H.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Orlando, B.J. et al., Crystal structure of rofecoxib bound to human cyclooxygenase-2. Acta Crystallogr.,Sect.F (2016)

Release Date

2016-09-28

Peptides

Prostaglandin G/H synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prostaglandin G/H synthase 2