SMTL ID : 3dqs.1

Structure of endothelial NOS heme domain in complex with a inhibitor (+-)-N1-{cis-4'-[(6"-amino-4"-methylpyridin-2"-yl)methyl]pyrrolidin-3'-yl}-N2-(4'-chlorobenzyl)ethane-1,2-diamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.1: 2 residues within 4Å: Chain A: W.258, C.318 No protein-ligand interaction detected (PLIP) CAC.8: 2 residues within 4Å: Chain B: W.258, C.318 No protein-ligand interaction detected (PLIP)

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

ACT.2: 6 residues within 4Å: Chain A: G.122, I.124, W.292, V.354, S.362 Ligands: HEM.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.362, A:S.362 ACT.9: 5 residues within 4Å: Chain B: G.122, W.292, V.354, S.362 Ligands: HEM.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.292, B:S.362 Water bridges: B:Q.125

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.30, C.35 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

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

HEM.4: 21 residues within 4Å: Chain A: W.114, A.117, R.119, C.120, V.121, G.122, L.129, S.162, M.275, F.289, S.290, W.292, M.294, E.297, V.354, W.383, F.409, Y.411 Ligands: ACT.2, H4B.5, JI3.6 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:W.114, A:W.114, A:W.114, A:A.117, A:F.289, A:F.289, A:F.289, A:W.292, A:V.354, A:W.383, A:F.409, A:F.409, A:F.409 Hydrogen bonds: A:Y.411 pi-Stacking: A:W.114 Metal complexes: A:C.120 HEM.10: 22 residues within 4Å: Chain B: W.114, A.117, R.119, C.120, V.121, G.122, L.129, S.162, M.275, F.289, S.290, G.291, W.292, M.294, E.297, V.354, W.383, F.409, Y.411 Ligands: ACT.9, H4B.11, JI3.12 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.114, B:W.114, B:W.114, B:A.117, B:R.119, B:F.289, B:F.289, B:F.289, B:F.289, B:W.292, B:V.354, B:W.383, B:F.409, B:F.409, B:F.409 Hydrogen bonds: B:R.119 pi-Stacking: B:W.114 Metal complexes: B:C.120

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

H4B.5: 12 residues within 4Å: Chain A: S.38, V.40, R.301, A.382, W.383 Chain B: W.381, F.396, H.397, Q.398, E.399 Ligands: HEM.4, GOL.7 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:E.399 Hydrogen bonds: A:R.301, A:A.382, A:W.383 Water bridges: A:S.38, A:R.301, A:W.383 pi-Stacking: A:W.383, A:W.383 H4B.11: 12 residues within 4Å: Chain A: W.381, F.396, H.397, Q.398, E.399 Chain B: S.38, V.40, R.301, A.382, W.383 Ligands: HEM.10, GOL.13 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.301, B:A.382, B:W.383 pi-Stacking: B:W.383, B:W.383 pi-Cation interactions: B:W.383 Hydrophobic interactions: A:E.399 Water bridges: A:H.397

2 x JI3: N-{(3S,4S)-4-[(6-AMINO-4-METHYLPYRIDIN-2-YL)METHYL]PYRROLIDIN-3-YL}-N'-(4-CHLOROBENZYL)ETHANE-1,2-DIAMINE(Non-covalent)

JI3.6: 15 residues within 4Å: Chain A: L.41, Q.183, P.270, V.272, F.289, S.290, G.291, W.292, Y.293, E.297, W.383, Y.411 Chain B: W.10 Ligands: HEM.4, GOL.7 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:W.10, A:L.41, A:P.270, A:F.289, A:Y.411 Hydrogen bonds: A:M.294, A:E.297, A:E.297 Water bridges: A:Q.183, A:N.302, A:N.302, A:N.302 JI3.12: 15 residues within 4Å: Chain A: W.10 Chain B: L.41, Q.183, P.270, V.272, F.289, S.290, G.291, W.292, Y.293, E.297, W.383, Y.411 Ligands: HEM.10, GOL.13 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.41, B:P.270, B:F.289, B:Y.411, A:W.10 Hydrogen bonds: B:M.294, B:E.297 Water bridges: B:Q.183, B:Q.183

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: V.40, R.301, H.307, W.383 Chain B: W.10 Ligands: H4B.5, JI3.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.301, A:R.301, A:H.307 Water bridges: A:R.308 GOL.13: 7 residues within 4Å: Chain A: W.10 Chain B: V.40, R.301, H.307, W.383 Ligands: H4B.11, JI3.12 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.301, B:R.301, B:H.307 Water bridges: B:D.305, A:H.397

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Igarashi, J. et al., Crystal structures of constitutive nitric oxide synthases in complex with de novo designed inhibitors. J.Med.Chem. (2009)

Release Date

2009-03-31

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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