SMTL ID : 9cvu.1 (1 other biounit)

Structure of human neuronal nitric oxide synthase R354A/G357D mutant heme domain bound with 4-methyl-6-(3-((methylamino)methyl)-5-(trifluoromethyl)phenyl)pyridin-2-amine dihydrochloride

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 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, 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.2, 01.3 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:W.113, A:W.113, A:W.113, A:A.116, A:R.118, A:V.120, A:L.128, A:F.288, A:F.288, A:F.288, A:W.291, A:W.291, A:E.296, A:W.382, A:F.408, 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: 20 residues within 4Å: Chain B: W.113, A.116, R.118, C.119, V.120, G.121, 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, 01.9 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:W.113, B:A.116, B:R.118, B:V.120, B:L.128, 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, B:F.408 Water bridges: 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: 11 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 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:E.398 Water bridges: B:H.396, A:S.38, A:R.300, A:R.300, A:R.300, A:W.382 Hydrogen bonds: A:R.300, A:V.381, A:W.382 pi-Stacking: A:W.382, A:W.382 pi-Cation interactions: A:W.382 H4B.8: 10 residues within 4Å: Chain A: W.380, F.395, H.396, Q.397, E.398 Chain B: S.38, R.300, V.381, W.382 Ligands: HEM.7 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 01: (6P)-4-methyl-6-{3-[(methylamino)methyl]-5-(trifluoromethyl)phenyl}pyridin-2-amine

01.3: 15 residues within 4Å: Chain A: Q.182, P.269, V.271, M.274, F.288, S.289, G.290, W.291, Y.292, M.293, E.296, D.301, W.382, Y.410 Ligands: HEM.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.269, A:V.271, A:F.288 Hydrogen bonds: A:M.293, A:E.296, A:E.296 Water bridges: A:Q.182, A:R.307 01.9: 13 residues within 4Å: Chain B: Q.182, P.269, V.271, M.274, F.288, S.289, G.290, W.291, Y.292, M.293, E.296, W.382 Ligands: HEM.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.269, B:V.271, B:F.288 Hydrogen bonds: B:M.293, B:E.296, B:E.296, B:E.296 Water bridges: B:Q.182

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: L.20, Q.68, R.373 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.68, A:R.373 Water bridges: A:K.23, A:E.64, A:Q.68, A:Q.68, A:R.114, A:R.114 GOL.5: 5 residues within 4Å: Chain A: I.106, 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:V.130, A:V.130 GOL.10: 3 residues within 4Å: Chain B: Q.68, R.373, T.405 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.373 Water bridges: B:K.23, B:Q.68, B:Q.68, B:R.114, B:T.405 GOL.11: 5 residues within 4Å: Chain B: I.106, K.110, L.128, Q.129, V.130 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.110, B:L.128, B:V.130, B:V.130 Water bridges: B:K.110

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 7 residues within 4Å: Chain A: C.30, C.35, M.36, G.37 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

Vasu, D. et al., Truncated pyridinylbenzylamines: Potent, selective, and highly membrane permeable inhibitors of human neuronal nitric oxide synthase. Bioorg.Med.Chem. (2025)

Release Date

2025-04-30

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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