SMTL ID : 5unw.1

Structure of rat neuronal nitric oxide synthase heme domain in complex with 3-[2-(2-amino-4-methylquinolin-7-yl)ethyl]-5-((methylamino)methyl)benzonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 20 residues within 4Å: Chain A: W.113, A.116, R.118, C.119, V.120, G.121, S.161, M.274, F.288, S.289, G.290, W.291, M.293, E.296, W.382, F.408, Y.410 Ligands: H4B.2, 8F7.3, ACT.4 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:W.113, A:W.113, A:A.116, A:R.118, A:F.288, A:F.288, A:W.291, A:E.296, A:W.382, A:F.408, A:F.408, A:F.408 Hydrogen bonds: A:Y.410 Salt bridges: A:R.118 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.6: 19 residues within 4Å: Chain B: W.113, A.116, R.118, C.119, V.120, G.121, M.274, F.288, S.289, G.290, W.291, M.293, E.296, W.382, F.408, Y.410 Ligands: H4B.7, 8F7.8, ACT.9 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:A.116, B:R.118, B:V.120, B:F.288, B:F.288, B:F.288, B:W.291, B:E.296, B:W.382, B:W.382, B:F.408, B:F.408 Hydrogen bonds: B:Y.410 Water bridges: B:R.300 Salt bridges: B:R.118, B:R.300 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, 8F7.3 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.300, A:V.381, A:W.382 pi-Stacking: A:W.382, A:W.382 Hydrophobic interactions: B:E.398 H4B.7: 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.6, 8F7.8 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.300, B:R.300, B:V.381, B:W.382, B:W.382 pi-Stacking: B:W.382, B:W.382 pi-Cation interactions: B:W.382 Hydrophobic interactions: A:E.398

2 x 8F7: 3-[2-(2-amino-4-methylquinolin-7-yl)ethyl]-5-[(methylamino)methyl]benzonitrile(Non-covalent)

8F7.3: 9 residues within 4Å: Chain A: P.269, V.271, F.288, W.291, Y.292, E.296, Y.410 Ligands: HEM.1, H4B.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.271, A:F.288, A:F.288 Hydrogen bonds: A:E.296, A:R.300 8F7.8: 12 residues within 4Å: Chain B: M.40, P.269, V.271, F.288, W.291, Y.292, E.296, R.300, W.382, Y.410 Ligands: HEM.6, H4B.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.269, B:V.271, B:F.288, B:F.288, B:W.382 Hydrogen bonds: B:M.293, B:E.296, B:R.300, B:R.300

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

ACT.4: 4 residues within 4Å: Chain A: W.291, V.353, S.361 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.291 Hydrogen bonds: A:S.361 ACT.9: 4 residues within 4Å: Chain B: Q.124, W.291, V.353 Ligands: HEM.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.124, B:W.291 Hydrogen bonds: B:W.291, B:S.361

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: C.30, C.35, M.36 Chain B: C.30, C.35 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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