SMTL ID : 4k5k.1

Structure of bovine endothelial nitric oxide synthase heme domain in complex with ((2S, 3S)-1,3-bis((6-(2,5-dimethyl-1H-pyrrol-1-yl)-4-methylpyridin-2-yl)methoxy)-2-aminobutane

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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, S.189, F.316, S.317, G.318, W.319, M.321, E.324, V.381, W.410, F.436, Y.438 Ligands: H4B.2, Q13.3 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:F.316, A:F.316, A:F.316, A:F.316, A:W.319, A:W.319, A:E.324, A:V.381, A:F.436, A:F.436, A:F.436 Hydrogen bonds: A:Y.438 Water bridges: A:E.324, A:R.328 Salt bridges: A:R.146 pi-Stacking: A:W.141 Metal complexes: A:C.147 HEM.8: 21 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, Q13.10, ACT.11 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: 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:E.324, B:V.381, B:W.410, B:F.436, B:F.436, B:F.436 Water bridges: B:Y.438 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 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.328, A:R.328, A:A.409, A:W.410 Water bridges: A:S.65, 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:A.409, B:W.410 Water bridges: B:R.328 pi-Stacking: B:W.410, B:W.410 Hydrophobic interactions: A:E.426

2 x Q13: 6,6'-{[(2S,3S)-2-aminobutane-1,3-diyl]bis(oxymethanediyl)}bis(4-methylpyridin-2-amine)(Non-covalent)

Q13.3: 14 residues within 4Å: Chain A: V.67, L.68, P.297, V.299, F.316, G.318, W.319, Y.320, M.321, E.324, W.410, Y.438 Ligands: HEM.1, ACT.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.68, A:P.297, A:V.299, A:F.316 Hydrogen bonds: A:M.321, A:E.324, A:Y.438, A:Y.438 Water bridges: A:N.301, A:E.324 Q13.10: 16 residues within 4Å: Chain A: W.37 Chain B: V.67, L.68, R.146, Q.210, P.297, V.299, F.316, G.318, W.319, Y.320, M.321, E.324, Y.438 Ligands: HEM.8, ACT.12 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.67, B:L.68, B:P.297, B:V.299, B:F.316, A:W.37 Hydrogen bonds: B:R.146, B:M.321, B:E.324, B:Y.438 Water bridges: B:N.301

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

ACT.4: 5 residues within 4Å: Chain A: G.149, Q.152, W.319, V.381, S.389 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.152 Hydrogen bonds: A:S.389, A:S.389 ACT.5: 5 residues within 4Å: Chain A: Q.210, R.213, N.329, R.335 Ligands: Q13.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.210 Water bridges: A:Y.294 Salt bridges: A:R.213, A:R.335 ACT.11: 6 residues within 4Å: Chain B: G.149, 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:W.319, B:S.389 ACT.12: 5 residues within 4Å: Chain B: Q.210, R.213, N.329, R.335 Ligands: Q13.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.210, B:N.329, 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.328, A:R.328, A:H.334 GOL.13: 6 residues within 4Å: Chain A: W.37 Chain B: V.67, R.328, H.334, W.410 Ligands: H4B.9 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: 5 residues within 4Å: Chain A: C.57, C.62, G.64 Chain B: C.57, C.62 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.57, A:C.62, B:C.57, B:C.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jing, Q. et al., Chiral linkers to improve selectivity of double-headed neuronal nitric oxide synthase inhibitors. Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-09-18

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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