SMTL ID : 3nli.1

Structure of endothelial nitric oxide synthase N368D mutant heme domain complexed with 6-{{(3'R,4'R)-3'-[2"-(3'''-fluorophenethylamino)ethoxy]pyrrolidin-4'-yl}methyl}-4-methylpyridin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: W.142, A.145, R.147, C.148, V.149, G.150, L.157, S.190, M.303, F.317, S.318, G.319, W.320, M.322, E.325, V.382, W.411, F.437 Ligands: H4B.2, ACT.3, JRR.5 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:W.142, A:W.142, A:W.142, A:A.145, A:L.157, A:F.317, A:F.317, A:F.317, A:F.317, A:W.320, A:W.320, A:V.382, A:F.437, A:F.437, A:F.437 Water bridges: A:R.147 pi-Stacking: A:W.142 Metal complexes: A:C.148 HEM.8: 21 residues within 4Å: Chain B: W.142, A.145, R.147, C.148, V.149, G.150, L.157, S.190, M.303, F.317, S.318, G.319, W.320, M.322, E.325, V.382, W.411, F.437 Ligands: H4B.9, ACT.10, JRR.12 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:W.142, B:W.142, B:W.142, B:A.145, B:F.317, B:F.317, B:F.317, B:F.317, B:W.320, B:V.382, B:F.437, B:F.437, B:F.437 Water bridges: B:R.147 pi-Stacking: B:W.142 Metal complexes: B:C.148

2 x H4B: 5,6,7,8-TETRAHYDROBIOPTERIN(Non-covalent)

H4B.2: 13 residues within 4Å: Chain A: S.66, V.68, R.329, A.410, W.411 Chain B: W.409, F.424, H.425, Q.426, E.427 Ligands: HEM.1, GOL.4, JRR.5 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.329, A:A.410, A:W.411 Water bridges: A:S.66, A:R.329, A:W.411 pi-Stacking: A:W.411, A:W.411 Hydrophobic interactions: B:E.427 H4B.9: 13 residues within 4Å: Chain A: W.409, F.424, H.425, Q.426, E.427 Chain B: S.66, V.68, R.329, A.410, W.411 Ligands: HEM.8, GOL.11, JRR.12 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.329, B:A.410, B:W.411 pi-Stacking: B:W.411, B:W.411 Hydrophobic interactions: A:E.427

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

ACT.3: 5 residues within 4Å: Chain A: G.150, W.320, V.382, S.390 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.320, A:S.390 ACT.10: 7 residues within 4Å: Chain B: G.150, I.152, Q.153, W.320, V.382, S.390 Ligands: HEM.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.153 Hydrogen bonds: B:S.390, B:S.390

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: R.329, H.335 Chain B: W.38 Ligands: H4B.2, JRR.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.329, A:R.329, A:H.335 GOL.11: 7 residues within 4Å: Chain A: W.38 Chain B: V.68, R.329, H.335, W.411 Ligands: H4B.9, JRR.12 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.329, B:R.329, B:H.335 Water bridges: B:D.333, A:H.425

2 x JRR: 6-{[(3R,4R)-4-(2-{[2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine(Non-covalent)

JRR.5: 16 residues within 4Å: Chain A: V.68, R.147, Q.211, P.298, V.300, F.317, S.318, G.319, W.320, E.325, W.411, Y.439 Chain B: W.38 Ligands: HEM.1, H4B.2, GOL.4 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.68, A:P.298, A:P.298, A:V.300, A:Y.439, A:Y.439, B:W.38 Hydrogen bonds: A:R.147, A:E.325 Water bridges: A:Q.211 JRR.12: 17 residues within 4Å: Chain A: W.38 Chain B: V.68, L.69, R.147, Q.211, P.298, V.300, F.317, S.318, G.319, W.320, E.325, W.411, Y.439 Ligands: HEM.8, H4B.9, GOL.11 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.68, B:L.69, B:P.298, B:V.300, B:Y.439, B:Y.439, A:W.38 Hydrogen bonds: B:R.147, B:E.325 Water bridges: B:Q.211

2 x CAD: CACODYLIC ACID(Non-covalent)

CAD.6: 2 residues within 4Å: Chain A: L.290, C.346 No protein-ligand interaction detected (PLIP) CAD.13: 2 residues within 4Å: Chain B: W.286, C.346 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: C.58, C.63, G.65 Chain B: C.58, C.63 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.58, B:C.63, A:C.58, A:C.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ji, H. et al., Exploration of the Active Site of Neuronal Nitric Oxide Synthase by the Design and Synthesis of Pyrrolidinomethyl 2-Aminopyridine Derivatives. J.Med.Chem. (2010)

Release Date

2010-11-03

Peptides

Nitric oxide synthase, endothelial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric oxide synthase, endothelial

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