SMTL ID : 8fgi.1

Structure of human neuronal nitric oxide synthase R354A/G357D mutant heme domain in complex with 4-(5-(2-(dimethylamino)ethyl)-2,3-difluorophenethyl)-6-methylpyrimidin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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, S.161, F.288, S.289, G.290, W.291, M.293, E.296, W.382, F.408, Y.410 Ligands: H4B.2, V80.3 18 PLIP interactions: 18 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: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, A:R.300 Salt bridges: A:R.118 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.7: 18 residues within 4Å: Chain B: W.113, A.116, R.118, C.119, V.120, L.128, S.161, F.288, S.289, G.290, W.291, M.293, E.296, W.382, F.408, Y.410 Ligands: H4B.8, V80.9 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:W.113, B:A.116, B:R.118, B:L.128, 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, B:F.408 Hydrogen bonds: B:Y.410 Water bridges: 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: 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 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.300, A:V.381, A:W.382 Water bridges: A:S.38, A:R.300, A:R.300, A:W.382 pi-Stacking: A:W.382, A:W.382 pi-Cation interactions: A:W.382 Hydrophobic interactions: B:E.398 H4B.8: 11 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 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 Water bridges: B:S.38, B:W.382 pi-Stacking: B:W.382, B:W.382 Hydrophobic interactions: A:E.398

2 x V80: 4-(2-{5-[2-(dimethylamino)ethyl]-2,3-difluorophenyl}ethyl)-6-methylpyrimidin-2-amine(Non-covalent)

V80.3: 13 residues within 4Å: Chain A: Q.182, 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.288, A:Y.292 Hydrogen bonds: A:W.291, A:M.293, A:R.307 Water bridges: A:R.300 Salt bridges: A:E.296, A:D.301 V80.9: 13 residues within 4Å: Chain B: Q.182, 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 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.288, B:Y.292, B:E.296 Hydrogen bonds: B:W.291, B:M.293 Water bridges: B:R.300 Salt bridges: B:E.296, B:D.301

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: L.20, Q.68, R.373 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.68, A:R.373 Water bridges: A:Q.68, A:Q.68, A:Y.107, A:Y.107 GOL.5: 5 residues within 4Å: Chain A: I.106, K.110, L.128, Q.129, V.130 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.110, A:Q.129, A:V.130 Water bridges: A:K.110, A:Q.129 GOL.10: 3 residues within 4Å: Chain B: L.20, Q.68, R.373 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.68, B:Q.68, B:R.373 Water bridges: B:R.114

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

Vasu, D. et al., Potent, Selective, and Membrane Permeable 2-Amino-4-Substituted Pyridine-Based Neuronal Nitric Oxide Synthase Inhibitors. J.Med.Chem. (2023)

Release Date

2023-10-11

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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