SMTL ID : 6nhc.1

Structure of human neuronal nitric oxide synthase R354A/G357D mutant heme domain in complex with (S)-6-(2,3-difluoro-5-(2-(1-methylazetidin-2-yl)ethyl)phenethyl)-4-methylpyridin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: W.113, A.116, R.118, C.119, V.120, G.121, L.128, S.161, F.288, S.289, G.290, W.291, E.296, W.382, F.408, Y.410 Ligands: H4B.2, KNV.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:W.113, A:W.113, A:W.113, A:A.116, A:V.120, A:F.288, A:F.288, A:F.288, A:F.288, A:W.291, A:E.296, A:W.382, A:W.382, A:F.408, A:F.408, A:F.408 Hydrogen bonds: A:R.118 Water bridges: A:R.300 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.7: 17 residues within 4Å: Chain B: W.113, R.118, C.119, V.120, S.161, F.288, S.289, G.290, W.291, M.293, E.296, V.353, W.382, F.408, Y.410 Ligands: H4B.8, KNV.9 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:W.113, B:R.118, B:V.120, B:F.288, B:F.288, B:W.291, B:E.296, B:V.353, B:W.382, B:F.408, B:F.408, B:F.408 Hydrogen bonds: B:R.118, B:Y.410 Water bridges: 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, KNV.3 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:E.398 Hydrogen bonds: A:R.300, A:V.381, A:W.382 Water bridges: A:S.38 pi-Stacking: A:W.382, A:W.382 pi-Cation interactions: 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, KNV.9 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.300, B:R.300, B:V.381, B:W.382 pi-Stacking: B:W.382, B:W.382 pi-Cation interactions: B:W.382 Hydrophobic interactions: A:E.398

2 x KNV: 6-[2-(2,3-difluoro-5-{2-[(2S)-1-methylazetidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine(Non-covalent)

KNV.3: 15 residues within 4Å: Chain A: Q.182, Y.266, P.269, V.271, F.288, S.289, G.290, W.291, Y.292, E.296, R.300, D.301, R.307 Ligands: HEM.1, H4B.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.269, A:F.288, A:Y.292, A:E.296, A:R.300 Hydrogen bonds: A:M.293, A:E.296 Water bridges: A:R.307 Halogen bonds: A:Y.266 KNV.9: 15 residues within 4Å: Chain B: Q.182, Y.266, P.269, V.271, F.288, S.289, G.290, W.291, Y.292, E.296, R.300, D.301, R.307 Ligands: HEM.7, H4B.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.288, B:E.296, B:R.300 Hydrogen bonds: B:M.293, B:E.296 Halogen bonds: B:Y.266

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: Q.68, R.373 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.68, A:R.373 GOL.5: 4 residues within 4Å: Chain A: K.110, L.128, Q.129, V.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.110, A:L.128, A:Q.129, A:V.130 GOL.10: 2 residues within 4Å: Chain B: Q.68, R.373 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.68, B:Q.68, B:R.373 Water bridges: B:K.23, B:H.111, B:R.114, B:T.405

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 A, 2 interactions with chain B Metal complexes: A:C.30, A:C.35, B:C.30, B:C.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Do, H.T. et al., Optimization of Blood-Brain Barrier Permeability with Potent and Selective Human Neuronal Nitric Oxide Synthase Inhibitors Having a 2-Aminopyridine Scaffold. J. Med. Chem. (2019)

Release Date

2019-03-13

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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