SMTL ID : 7tsc.1

Structure of rat neuronal nitric oxide synthase R349A mutant heme domain in complex with 4-methyl-6-(3-(4-methylpiperazin-1-yl)propyl)pyridin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 19 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, KMR.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:E.296, A:W.382, 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.300 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.6: 19 residues within 4Å: Chain B: 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.7, KMR.8 20 PLIP interactions: 20 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: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 Water bridges: B:R.300, 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: 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 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.300, A:R.300, A:V.381, A:W.382 Water bridges: A:I.39, B:H.396 pi-Stacking: A:W.382, A:W.382 pi-Cation interactions: A:W.382 Hydrophobic interactions: B:E.398 H4B.7: 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.6 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:E.398 Water bridges: A:H.396, B:I.39 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

2 x KMR: 4-methyl-6-[3-(4-methylpiperazin-1-yl)propyl]pyridin-2-amine(Non-covalent)

KMR.3: 10 residues within 4Å: Chain A: P.269, V.271, F.288, S.289, G.290, W.291, Y.292, E.296, W.382 Ligands: HEM.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.269, A:F.288 Hydrogen bonds: A:E.296 Water bridges: A:N.273 KMR.8: 10 residues within 4Å: Chain B: P.269, V.271, F.288, S.289, G.290, W.291, Y.292, E.296, W.382 Ligands: HEM.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.269, B:F.288 Hydrogen bonds: B:E.296 Water bridges: B:N.273

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

ACT.4: 7 residues within 4Å: Chain A: G.121, I.123, Q.124, W.291, V.353, A.358, S.361 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.123, A:Q.124 Hydrogen bonds: A:S.361 ACT.9: 7 residues within 4Å: Chain B: G.121, I.123, Q.124, W.291, V.353, A.358, S.361 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.123, B:Q.124 Hydrogen bonds: B:S.361

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: C.30, C.35, M.36 Chain B: C.30, C.35 Ligands: ZN.10 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.30, B:C.35, A:C.30, A:C.35 ZN.10: 6 residues within 4Å: Chain A: C.30, C.35 Chain B: C.30, C.35, M.36 Ligands: ZN.5 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.30, B:C.35, A:C.30, A:C.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vasu, D. et al., 2-Aminopyridines with a shortened amino sidechain as potent, selective, and highly permeable human neuronal nitric oxide synthase inhibitors. Bioorg.Med.Chem. (2022)

Release Date

2022-07-13

Peptides

Nitric oxide synthase, brain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Nitric oxide synthase, brain

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