SMTL ID : 4d3a.1

Structure of bovine endothelial nitric oxide synthase heme domain in complex with 3-(3-fluorophenyl)-N-2-(2-(5-methyl-1H-imidazol-1-yl) pyrimidin-4-yl)ethylpropan-1-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: 19 residues within 4Å: Chain A: W.141, A.144, R.146, C.147, V.148, G.149, L.156, S.189, F.316, S.317, G.318, W.319, M.321, E.324, W.410, F.436, Y.438 Ligands: H4B.2, 7F5.3 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:W.141, A:W.141, A:W.141, A:A.144, A:R.146, A:L.156, A:F.316, A:F.316, A:F.316, A:F.316, A:W.319, A:W.319, A:E.324, A:W.410, A:W.410, A:F.436, A:F.436, A:F.436 Hydrogen bonds: A:Y.438 Salt bridges: A:R.146 pi-Stacking: A:W.141 Metal complexes: A:C.147 HEM.8: 20 residues within 4Å: Chain B: W.141, A.144, R.146, C.147, V.148, G.149, S.189, M.302, F.316, S.317, G.318, W.319, M.321, E.324, V.381, W.410, F.436, Y.438 Ligands: H4B.9, 7F5.10 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:W.141, B:W.141, B:W.141, B:A.144, B:R.146, B:F.316, B:F.316, B:F.316, B:F.316, B:W.319, B:V.381, B:W.410, B:F.436, B:F.436, B:F.436 Water bridges: B:R.146, B:Y.438 Salt bridges: B:R.146 pi-Stacking: B:W.141 Metal complexes: B:C.147

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

H4B.2: 12 residues within 4Å: Chain A: S.65, V.67, R.328, A.409, W.410 Chain B: W.408, F.423, H.424, Q.425, E.426 Ligands: HEM.1, GOL.6 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.328, A:R.328, A:A.409, A:W.410 pi-Stacking: A:W.410, A:W.410 pi-Cation interactions: A:W.410 Hydrophobic interactions: B:E.426 H4B.9: 12 residues within 4Å: Chain A: W.408, F.423, H.424, Q.425, E.426 Chain B: S.65, V.67, R.328, A.409, W.410 Ligands: HEM.8, GOL.13 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.328, B:R.328, B:A.409, B:W.410 pi-Stacking: B:W.410, B:W.410 Hydrophobic interactions: A:E.426

2 x 7F5: 3-(3-fluorophenyl)-N-{2-[2-(5-methyl-1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}propan-1-amine(Non-covalent)

7F5.3: 15 residues within 4Å: Chain A: V.67, L.68, Q.210, P.297, A.298, V.299, F.316, S.317, G.318, E.324, Y.438 Chain B: W.37 Ligands: HEM.1, ACT.5, GOL.6 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.67, A:L.68, A:P.297, A:V.299, B:W.37 Hydrogen bonds: A:E.324 7F5.10: 14 residues within 4Å: Chain A: W.37 Chain B: L.68, Q.210, P.297, A.298, V.299, F.316, S.317, E.324, W.410, Y.438 Ligands: HEM.8, ACT.12, GOL.13 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.68, B:P.297, B:V.299, B:W.410, A:W.37

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

ACT.4: 4 residues within 4Å: Chain A: G.149, W.319, V.381, S.389 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.319, A:S.389 Water bridges: A:Q.152 ACT.5: 7 residues within 4Å: Chain A: Q.210, R.213, Y.294, Y.320, N.329, R.335 Ligands: 7F5.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.210, A:Y.294, A:N.329 Water bridges: A:R.213, A:R.335 Salt bridges: A:R.213, A:R.335 ACT.11: 6 residues within 4Å: Chain B: G.149, I.151, Q.152, W.319, V.381, S.389 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.152, B:W.319 Hydrogen bonds: B:S.389, B:S.389 ACT.12: 8 residues within 4Å: Chain B: Q.210, R.213, Y.294, Y.320, E.324, N.329, R.335 Ligands: 7F5.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.210, B:Y.320, B:N.329 Water bridges: B:R.213, B:Y.294 Salt bridges: B:R.213, B:R.335

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: V.67, R.328, H.334, W.410 Chain B: W.37 Ligands: H4B.2, 7F5.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.328, A:R.328, A:H.334 GOL.13: 7 residues within 4Å: Chain A: W.37 Chain B: V.67, R.328, H.334, W.410 Ligands: H4B.9, 7F5.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.328, B:R.328, B:H.334 Water bridges: A:H.424

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: C.57, C.62 Chain B: C.57, C.62, G.64 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.57, B:C.62, A:C.57, A:C.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mukherjee, P. et al., Novel 2,4-Disubstituted Pyrimidines as Potent, Selective, and Cell-Permeable Inhibitors of Neuronal Nitric Oxide Synthase. J.Med.Chem. (2015)

Release Date

2014-12-24

Peptides

NITRIC OXIDE SYNTHASE, ENDOTHELIAL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NITRIC OXIDE SYNTHASE, ENDOTHELIAL

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