SMTL ID : 6ngu.1

Structure of rat neuronal nitric oxide synthase heme domain in complex with 6-(3-(3-(dimethylamino)propyl)-2,5-difluorophenethyl)-4-methylpyridin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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, KMJ.3, ACT.4 19 PLIP interactions: 19 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 Water bridges: A:E.296, A:R.300, A:R.403 Salt bridges: A:R.118 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.6: 18 residues within 4Å: Chain B: W.113, A.116, R.118, C.119, 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.7, KMJ.8 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:A.116, 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 Hydrogen bonds: B:Y.410 Water bridges: B:E.296, B:E.296, 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: 10 residues within 4Å: Chain A: S.38, R.300, V.381, W.382 Chain B: W.380, F.395, H.396, Q.397, E.398 Ligands: HEM.1 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: 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.6 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:E.398 Hydrogen bonds: B:R.300, B:R.300, B:V.381, B:W.382 Water bridges: B:I.39, B:W.382 pi-Stacking: B:W.382, B:W.382 pi-Cation interactions: B:W.382

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

KMJ.3: 12 residues within 4Å: Chain A: M.40, P.269, V.271, M.274, F.288, S.289, G.290, W.291, Y.292, E.296, W.382 Ligands: HEM.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.269, A:V.271, A:F.288 Hydrogen bonds: A:M.293, A:E.296 KMJ.8: 12 residues within 4Å: Chain B: M.40, Q.182, P.269, V.271, M.274, F.288, G.290, W.291, Y.292, E.296, Y.410 Ligands: HEM.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.269, B:V.271, B:V.271, B:F.288 Hydrogen bonds: B:M.293, B:E.296

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

ACT.4: 3 residues within 4Å: Chain A: W.291, 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: 6 residues within 4Å: Chain B: G.121, I.123, Q.124, W.291, V.353, S.361 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.123, B:Q.124 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 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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