SMTL ID : 8fgf.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 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, XVO.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:F.288, A:F.288, A:F.288, A:W.291, 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, A:R.300 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, G.121, 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, XVO.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:V.120, B:L.128, 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 12 PLIP interactions: 11 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:R.300, A:W.382, B:H.396 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, XVO.9 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.300, B:V.381, B:W.382 Water bridges: B:S.38, B:R.300, B:R.300, B:R.300, B:W.382, A:H.396 pi-Stacking: B:W.382, B:W.382 pi-Cation interactions: B:W.382 Hydrophobic interactions: A:E.398

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

XVO.3: 11 residues within 4Å: Chain A: Q.182, R.185, Y.266, P.269, A.270, V.271, W.291, Y.292, M.293, E.296 Ligands: HEM.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.182, A:P.269, A:V.271 Hydrogen bonds: A:M.293, A:E.296 Water bridges: A:R.307 Halogen bonds: A:Y.266 XVO.9: 12 residues within 4Å: Chain B: M.40, P.269, V.271, M.274, F.288, W.291, Y.292, M.293, E.296, W.382 Ligands: HEM.7, H4B.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.269, B:V.271 Hydrogen bonds: B:M.293, B:E.296

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: Q.68, R.373 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.68, A:R.373 Water bridges: A:Q.68, A:Q.68, 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:V.130, A:V.130 Water bridges: A:Q.129 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:Q.68, B:R.373 Water bridges: B:K.23, B:N.115, B:T.405

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: C.30, C.35 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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