SMTL ID : 5uo6.1

Structure of human neuronal nitric oxide synthase heme domain in complex with (R)-3-[(2-amino-4-methylquinolin-7-yl)methoxy]-5-(2-(methylamino)propyl)benzonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 16 residues within 4Å: Chain A: W.113, R.118, C.119, V.120, S.161, F.288, S.289, G.290, W.291, M.293, E.296, W.382, F.408, Y.410 Ligands: H4B.2, M4R.3 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:W.113, A:W.113, A:R.118, A:V.120, A:F.288, A:F.288, A:F.288, A:W.291, A:E.296, A:W.382, A:F.408, A:F.408 Water bridges: A:R.300, A:R.300 Salt bridges: A:R.118 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.7: 19 residues within 4Å: Chain B: W.113, A.116, R.118, C.119, V.120, L.128, S.161, M.274, F.288, S.289, G.290, W.291, M.293, E.296, W.382, F.408, Y.410 Ligands: H4B.8, M4R.9 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:A.116, B:R.118, B:V.120, B:L.128, B:F.288, B:F.288, B:F.288, B:W.291, B:E.296, B:W.382, B:F.408, B:F.408 Hydrogen bonds: B:Y.410 Water bridges: B:E.296, B:R.300, B:R.300 Salt bridges: B:R.118 pi-Stacking: B:W.113 Metal complexes: B:C.119

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

H4B.2: 12 residues within 4Å: Chain A: S.38, M.40, R.300, V.381, W.382 Chain B: W.380, F.395, H.396, Q.397, E.398 Ligands: HEM.1, M4R.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.300, A:V.381, A:W.382 Water bridges: A:S.38, A:R.300, A:R.300, A:R.300, A:W.382 pi-Stacking: A:W.382, A:W.382 pi-Cation interactions: A:W.382, A:W.382 H4B.8: 12 residues within 4Å: Chain A: W.380, F.395, H.396, Q.397, E.398 Chain B: S.38, M.40, R.300, V.381, W.382 Ligands: HEM.7, M4R.9 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.300, B:R.300, B:V.381, B:W.382 Water bridges: B:S.38, B:W.382 pi-Stacking: B:W.382, B:W.382 pi-Cation interactions: B:W.382 Hydrophobic interactions: A:E.398

2 x M4R: 3-[(2-amino-4-methylquinolin-7-yl)methoxy]-5-[(2R)-2-(methylamino)propyl]benzonitrile(Non-covalent)

M4R.3: 12 residues within 4Å: Chain A: P.269, V.271, N.273, F.288, G.290, W.291, Y.292, E.296, W.382, Y.410 Ligands: HEM.1, H4B.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.269, A:V.271, A:F.288, A:F.288, A:W.382, A:Y.410 Hydrogen bonds: A:N.273, A:E.296 Water bridges: A:R.300 M4R.9: 12 residues within 4Å: Chain B: P.269, V.271, N.273, F.288, G.290, W.291, Y.292, E.296, W.382, Y.410 Ligands: HEM.7, H4B.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.271, B:F.288, B:F.288, B:W.382, B:Y.410 Hydrogen bonds: B:N.273, B:E.296 Water bridges: B:Q.182

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.114, C.372, R.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.114, A:R.114, A:C.372 GOL.5: 2 residues within 4Å: Chain A: Q.68, R.373 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.68, A:R.373 Water bridges: A:K.23, A:Q.68, A:Q.68, A:Y.107, A:Y.107, A:Y.107, A:R.114, A:T.405 GOL.10: 2 residues within 4Å: Chain B: Q.68, R.373 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.68, B:R.373 Water bridges: B:K.23, B:R.114, B:T.405, B:T.405 GOL.11: 6 residues within 4Å: Chain B: I.106, K.110, S.126, L.128, Q.129, V.130 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.110, B:L.128, B:V.130, B:V.130

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: C.30, C.35, M.36 Chain B: C.30, C.35, M.36 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.30, B:C.35, A:C.30, A:C.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cinelli, M.A. et al., Nitrile in the Hole: Discovery of a Small Auxiliary Pocket in Neuronal Nitric Oxide Synthase Leading to the Development of Potent and Selective 2-Aminoquinoline Inhibitors. J. Med. Chem. (2017)

Release Date

2017-05-03

Peptides

Nitric oxide synthase, brain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric oxide synthase, brain

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