SMTL ID : 4upm.1

Structure of rat neuronal nitric oxide synthase heme domain in complex with N',N'-{[(2R)-3-aminopropane-1,2-diyl]bis(oxymethanediylbenzene-3,1-diyl)}dithiophene-2-carboximidamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 20 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, V.353, W.382, F.408, Y.410 Ligands: H4B.2, I5U.3, ACT.4 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:W.113, A:W.113, A:W.113, A:A.116, A:R.118, A:F.288, A:F.288, A:F.288, A:F.288, A:W.291, A:W.291, A:E.296, A:V.353, A:W.382, 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 Salt bridges: A:R.118 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.6: 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, V.353, W.382, F.408, Y.410 Ligands: H4B.7, I5U.8 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:W.113, B:A.116, B:F.288, B:F.288, B:F.288, B:F.288, B:W.291, B:W.291, B:E.296, B:V.353, B:W.382, B:F.408, B:F.408 Water bridges: B:E.296, B:R.300, B:R.300 Salt bridges: B:R.118 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 12 PLIP interactions: 11 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:R.300, A:R.300, A:W.382 pi-Stacking: A:W.382, A:W.382 pi-Cation interactions: A:W.382, 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 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:E.398 Water bridges: A:H.396, B:R.300, B:R.300, B:R.300 Hydrogen bonds: 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 I5U: N',N'-{[(2R)-3-aminopropane-1,2-diyl]bis(oxymethanediylbenzene-3,1-diyl)}dithiophene-2-carboximidamide(Non-covalent)

I5U.3: 15 residues within 4Å: Chain A: M.40, Q.182, P.269, V.271, F.288, S.289, G.290, W.291, Y.292, E.296, S.306, W.382, Y.410 Chain B: W.10 Ligands: HEM.1 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.269, A:V.271, A:V.271, A:F.288, B:W.10, B:W.10 Hydrogen bonds: A:E.296 I5U.8: 14 residues within 4Å: Chain A: W.10 Chain B: Q.182, R.185, P.269, V.271, F.288, S.289, G.290, W.291, Y.292, E.296, W.382, Y.410 Ligands: HEM.6 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.269, B:V.271, B:F.288, A:W.10, A:W.10 Hydrogen bonds: B:R.185, B:E.296 Water bridges: B:Q.182, B:N.273

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

ACT.4: 6 residues within 4Å: Chain A: G.121, Q.124, W.291, V.353, S.361 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.124, A:W.291 Hydrogen bonds: A:W.291 ACT.9: 4 residues within 4Å: Chain B: G.121, Q.124, W.291, V.353 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.124 Water bridges: B:Q.124, B:S.361

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jing, Q. et al., Combination of Chiral Linkers with Thiophenecarboximidamide Heads to Improve the Selectivity of Inhibitors of Neuronal Nitric Oxide Synthase. Bioorg.Med.Chem.Lett. (2014)

Release Date

2014-08-20

Peptides

NEURONAL NITRIC OXIDE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NEURONAL NITRIC OXIDE SYNTHASE

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