SMTL ID : 3nlp.1

Structure of neuronal nitric oxide synthase D597N/M336V mutant heme domain in complex with 6-{{(3'S,4'S)-3'-[2"-(3'''-fluorophenethylamino)ethoxy]pyrrolidin-4'-yl}methyl}-4-methylpyridin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: W.113, A.116, R.118, C.119, V.120, G.121, L.128, S.161, M.274, F.288, S.289, G.290, W.291, M.293, E.296, W.382, F.408, Y.410 Ligands: H4B.3, JSS.4, ACT.5 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:W.113, A:W.113, A:A.116, A:R.118, A:V.120, A:L.128, A:F.288, A:F.288, A:F.288, A:W.291, A:E.296, A:F.408, A:F.408 Hydrogen bonds: A:Y.410 Water bridges: A:R.300 Salt bridges: A:R.118 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.8: 20 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.9, JSS.10, ACT.11 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:W.113, B:A.116, B:V.120, B:F.288, B:F.288, B:F.288, B:W.291, B:E.296, B:F.408, B:F.408 Water bridges: B:R.300 Salt bridges: B:R.118 pi-Stacking: B:W.113 Metal complexes: B:C.119

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.300, W.382 Chain B: W.10 Ligands: H4B.3, JSS.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.300, A:R.300 GOL.6: 4 residues within 4Å: Chain A: W.10, H.396 Chain B: R.300 Ligands: H4B.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.300, B:R.300, A:H.396

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

H4B.3: 12 residues within 4Å: Chain A: S.38, V.40, R.300, V.381, W.382 Chain B: W.380, F.395, H.396, Q.397, E.398 Ligands: HEM.1, GOL.2 8 PLIP interactions: 7 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:W.382 pi-Stacking: A:W.382, A:W.382 Hydrophobic interactions: B:E.398 H4B.9: 12 residues within 4Å: Chain A: W.380, F.395, H.396, Q.397, E.398 Chain B: S.38, V.40, R.300, V.381, W.382 Ligands: GOL.6, HEM.8 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:E.398 Hydrogen bonds: B:R.300, B:V.381, B:W.382 pi-Stacking: B:W.382, B:W.382

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

JSS.4: 15 residues within 4Å: Chain A: V.40, Q.182, P.269, V.271, F.288, S.289, G.290, W.291, Y.292, E.296, W.382, Y.410 Chain B: W.10 Ligands: HEM.1, GOL.2 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.40, A:P.269, A:F.288, A:W.382, B:W.10, B:W.10 Hydrogen bonds: A:M.293, A:E.296, A:E.296 Water bridges: A:Q.182, A:Q.182, A:N.301 JSS.10: 16 residues within 4Å: Chain A: W.10 Chain B: V.40, L.41, Q.182, P.269, V.271, F.288, S.289, G.290, W.291, Y.292, M.293, E.296, W.382, Y.410 Ligands: HEM.8 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.40, B:L.41, B:P.269, B:V.271, B:F.288, B:W.382, A:W.10 Hydrogen bonds: B:M.293, B:E.296 Water bridges: B:Q.182, B:Q.182

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

ACT.5: 4 residues within 4Å: Chain A: I.123, W.291, S.361 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.291 Hydrogen bonds: A:W.291, A:S.361 ACT.11: 4 residues within 4Å: Chain B: G.121, W.291, S.361 Ligands: HEM.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.361

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 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

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, brain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric oxide synthase, brain

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