SMTL ID : 4ups.1

Structure of bovine endothelial nitric oxide synthase heme domain in complex with N-[3-({[(3S,5S)-5-{[(3-{[(Z)-imino(thiophen-2-yl)methyl]amino}benzyl)oxy]methyl}pyrrolidin-3-yl]oxy}methyl) phenyl]thiophene-2-carboximidamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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, W.319, E.324, V.381, W.410, F.436, Y.438 Ligands: H4B.2, 6E5.3, ACT.4 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:V.381, A:W.410, A:F.436, A:F.436 Hydrogen bonds: A:Y.438 Water bridges: A:E.324 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, L.156, S.189, M.302, F.316, S.317, W.319, E.324, V.381, W.410, F.436, Y.438 Ligands: H4B.9, 6E5.10, ACT.11 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:L.156, B:F.316, B:F.316, B:F.316, B:F.316, B:W.319, B:E.324, B:V.381, B:W.410, B:F.436, B:F.436, B:F.436 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:A.409, A:W.410 Water bridges: A:R.328 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 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.328, B:A.409, B:W.410 Water bridges: B:R.328 pi-Stacking: B:W.410, B:W.410 pi-Cation interactions: B:W.410 Hydrophobic interactions: A:E.426

2 x 6E5: N-[3-({[(3S,5S)-5-{[(3-{[(Z)-imino(thiophen-2-yl)methyl]amino}benzyl)oxy]methyl}pyrrolidin-3-yl]oxy}methyl)phenyl]thiophene-2-carboximidamide(Non-covalent)

6E5.3: 17 residues within 4Å: Chain A: L.68, Q.210, P.297, V.299, N.301, F.316, S.317, G.318, W.319, Y.320, E.324, W.410, Y.438, Q.439, P.440, D.441 Ligands: HEM.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.297, A:V.299, A:V.299, A:F.316, A:P.440 Hydrogen bonds: A:W.319, A:E.324, A:Q.439 Water bridges: A:Q.210, A:N.301, A:Q.439 6E5.10: 16 residues within 4Å: Chain B: L.68, Q.210, P.297, V.299, F.316, S.317, G.318, W.319, Y.320, E.324, W.410, Y.438, Q.439, P.440 Ligands: HEM.8, GOL.13 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.68, B:P.297, B:V.299, B:F.316, B:P.440 Hydrogen bonds: B:W.319, B:E.324, B:Q.439 Water bridges: B:Q.210

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

ACT.4: 7 residues within 4Å: Chain A: G.149, I.151, Q.152, W.319, V.381, S.389 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.152 Hydrogen bonds: A:W.319, A:S.389 ACT.5: 4 residues within 4Å: Chain A: Q.210, R.213, N.329, R.335 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.210, A:N.329 Salt bridges: A:R.213, A:R.335 ACT.11: 7 residues within 4Å: Chain B: G.149, I.151, Q.152, W.319, V.381, S.389 Ligands: HEM.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.152 Hydrogen bonds: B:S.389, B:S.389 ACT.12: 4 residues within 4Å: Chain B: Q.210, R.213, N.329, R.335 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.210, B:N.329 Salt bridges: B:R.213, B:R.335

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: V.67, R.328, H.334, W.410 Chain B: W.37 Ligands: H4B.2 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:H.424 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, 6E5.10 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:H.424, B:D.332 Hydrogen bonds: B:R.328, B:R.328, B:H.334

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: C.57, C.62 Chain B: C.57, C.62 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

Jing, Q. et al., Combination of Chiral Linkers with Thiophenecarboximidamide Heads to Improve the Selectivity of Inhibitors of Neuronal Nitric Oxide Synthase. Bioorg.Med.Chem.Lett. (2014)

Release Date

2014-08-20

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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