SMTL ID : 4luw.1

Structure of bovine endothelial nitric oxide synthase heme domain in complex with 6-((((3R,5S)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: W.140, A.143, R.145, C.146, V.147, G.148, L.155, S.188, F.315, S.316, W.318, E.323, W.409, F.435, Y.437 Ligands: H4B.2, QJ8.3, ACT.4 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:W.140, A:W.140, A:A.143, A:R.145, A:V.147, A:L.155, A:F.315, A:F.315, A:F.315, A:F.315, A:W.318, A:W.318, A:E.323, A:F.435, A:F.435 Hydrogen bonds: A:Y.437 Water bridges: A:E.323, A:R.327 pi-Stacking: A:W.140 Metal complexes: A:C.146 HEM.8: 21 residues within 4Å: Chain B: W.140, A.143, R.145, C.146, V.147, G.148, L.155, S.188, F.315, S.316, G.317, W.318, M.320, E.323, V.380, W.409, F.435, Y.437 Ligands: H4B.9, QJ8.10, ACT.11 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:W.140, B:W.140, B:A.143, B:R.145, B:L.155, B:F.315, B:F.315, B:F.315, B:W.318, B:E.323, B:V.380, B:W.409, B:F.435, B:F.435 pi-Stacking: B:W.140 Metal complexes: B:C.146

2 x H4B: 5,6,7,8-TETRAHYDROBIOPTERIN(Non-covalent)

H4B.2: 12 residues within 4Å: Chain A: S.64, V.66, R.327, A.408, W.409 Chain B: W.407, F.422, H.423, Q.424, E.425 Ligands: HEM.1, GOL.6 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.327, A:R.327, A:A.408, A:W.409 pi-Stacking: A:W.409, A:W.409 pi-Cation interactions: A:W.409 Hydrophobic interactions: B:E.425 H4B.9: 12 residues within 4Å: Chain A: W.407, F.422, H.423, Q.424, E.425 Chain B: S.64, V.66, R.327, A.408, W.409 Ligands: HEM.8, GOL.13 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.327, B:R.327, B:A.408, B:W.409 pi-Stacking: B:W.409, B:W.409 pi-Cation interactions: B:W.409, B:W.409 Hydrophobic interactions: A:E.425

2 x QJ8: 6-({[(3R,5S)-5-{[(6-amino-4-methylpyridin-2-yl)methoxy]methyl}pyrrolidin-3-yl]oxy}methyl)-4-methylpyridin-2-amine(Non-covalent)

QJ8.3: 13 residues within 4Å: Chain A: P.296, V.298, N.300, F.315, S.316, G.317, W.318, Y.319, M.320, E.323, Y.437, Q.438 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.296, A:F.315 Hydrogen bonds: A:M.320, A:E.323 Water bridges: A:N.300, A:Q.438 QJ8.10: 13 residues within 4Å: Chain A: W.36 Chain B: V.66, L.67, P.296, V.298, F.315, G.317, W.318, Y.319, M.320, E.323 Ligands: HEM.8, ACT.12 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.66, B:L.67, B:P.296, B:V.298, B:F.315, A:W.36, A:W.36 Hydrogen bonds: B:M.320, B:E.323 Water bridges: B:N.300

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: G.148, W.318, V.380, S.388 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.388, A:S.388 ACT.5: 3 residues within 4Å: Chain A: R.212, N.328, R.334 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.209 Water bridges: A:N.328 Salt bridges: A:R.212, A:R.334 ACT.11: 7 residues within 4Å: Chain B: G.148, I.150, Q.151, W.318, V.380, S.388 Ligands: HEM.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.151 Hydrogen bonds: B:W.318, B:S.388 ACT.12: 5 residues within 4Å: Chain B: Q.209, R.212, N.328, R.334 Ligands: QJ8.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.209, B:N.328 Water bridges: B:N.328 Salt bridges: B:R.212, B:R.334

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: V.66, R.327, H.333 Chain B: W.36 Ligands: H4B.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.327, A:R.327, A:H.333 GOL.13: 5 residues within 4Å: Chain A: W.36 Chain B: V.66, R.327, H.333 Ligands: H4B.9 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.327, B:R.327, B:H.333 Water bridges: B:D.331, A:H.423

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: C.56, C.61 Chain B: C.56, C.61 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.56, A:C.61, B:C.56, B:C.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holden, J.K. et al., Structural and biological studies on bacterial nitric oxide synthase inhibitors. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-10-23

Peptides

Nitric oxide synthase, endothelial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric oxide synthase, endothelial