SMTL ID : 3b3n.1

Structure of neuronal NOS heme domain in complex with a inhibitor (+-)-N1-{cis-4'-[(6"-aminopyridin-2"-yl)methyl]pyrrolidin-3'-yl}ethane-1,2-diamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 5 residues within 4Å: Chain A: Q.124, W.291, V.353, S.361 Ligands: HEM.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.124, A:W.291 Hydrogen bonds: A:S.361 ACT.6: 5 residues within 4Å: Chain B: G.121, Q.124, W.291, V.353 Ligands: HEM.7 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.124, B:W.291 Hydrogen bonds: B:W.291 Water bridges: B:Q.124

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 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 B, 2 interactions with chain A Metal complexes: B:C.30, B:C.35, A:C.30, A:C.35

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

HEM.3: 19 residues within 4Å: Chain A: W.113, A.116, R.118, C.119, V.120, S.161, M.274, F.288, S.289, G.290, W.291, M.293, E.296, W.382, F.408, Y.410 Ligands: ACT.1, H4B.4, JI2.5 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:W.113, A:W.113, A:A.116, A:F.288, A:F.288, 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:R.300, A:R.300 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.7: 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: ACT.6, H4B.8, JI2.9 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:A.116, B:R.118, B:F.288, 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, B:R.300 pi-Stacking: B:W.113 Metal complexes: B:C.119

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

H4B.4: 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.3 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:E.398 Water bridges: B:H.396 Hydrogen bonds: A:R.300, A:R.300, A:V.381, A:W.382 pi-Stacking: A:W.382, A:W.382 pi-Cation interactions: A:W.382, A:W.382 H4B.8: 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.7 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A 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, B:W.382 Hydrophobic interactions: A:E.398

2 x JI2: N-{(3S,4S)-4-[(6-aminopyridin-2-yl)methyl]pyrrolidin-3-yl}ethane-1,2-diamine(Non-covalent)

JI2.5: 7 residues within 4Å: Chain A: Q.182, P.269, V.271, W.291, Y.292, E.296 Ligands: HEM.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.269, A:V.271 Hydrogen bonds: A:E.296 Water bridges: A:Q.182, A:Y.266, A:N.273, A:N.273 JI2.9: 7 residues within 4Å: Chain B: Q.182, P.269, V.271, W.291, Y.292, E.296 Ligands: HEM.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.269 Hydrogen bonds: B:E.296, B:E.296 Water bridges: B:Q.182, B:Y.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ji, H. et al., Minimal pharmacophoric elements and fragment hopping, an approach directed at molecular diversity and isozyme selectivity. Design of selective neuronal nitric oxide synthase inhibitors. J.Am.Chem.Soc. (2008)

Release Date

2008-07-15

Peptides

Nitric-oxide synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric-oxide synthase

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