SMTL ID : 4v3u.1

Structure of human nNOS R354A G357D mutant heme domain in complex with N-2-(2-(1H-imidazol-1-yl)pyrimidin-4-yl)ethyl-3-(pyridin-3-yl) propan-1-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: 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.2, EG8.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:W.113, 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:W.382, A:F.408, A:F.408, A:F.408 Water bridges: A:R.300, A:R.300, A:Y.410 pi-Stacking: A:W.113 Metal complexes: A:C.119 HEM.6: 18 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, E.296, W.382, F.408, Y.410 Ligands: H4B.7, EG8.8 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.113, B:W.113, B:A.116, B:R.118, B:V.120, B:F.288, B:F.288, B:F.288, B:W.291, B:W.291, B:E.296, B:W.382, B:F.408, B:F.408 Water bridges: B:R.300, B:Y.410 pi-Stacking: B:W.113 Metal complexes: B:C.119 HEM.10: 20 residues within 4Å: Chain C: 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.11, EG8.12 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:W.113, C:W.113, C:A.116, C:L.128, C:F.288, C:F.288, C:F.288, C:F.288, C:W.291, C:E.296, C:F.408, C:F.408, C:F.408 Hydrogen bonds: C:Y.410 Water bridges: C:R.300, C:R.300, C:Y.410 pi-Stacking: C:W.113 Metal complexes: C:C.119 HEM.16: 19 residues within 4Å: Chain D: 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, E.296, W.382, F.408, Y.410 Ligands: H4B.17, EG8.18 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:W.113, D:W.113, D:W.113, D:A.116, D:R.118, D:V.120, D:L.128, D:F.288, D:F.288, D:F.288, D:F.288, D:W.291, D:E.296, D:F.408, D:F.408 Hydrogen bonds: D:Y.410 Water bridges: D:R.300, D:R.300, D:Y.410 pi-Stacking: D:W.113 Metal complexes: D:C.119

4 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 11 PLIP interactions: 10 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 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 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:E.398 Hydrogen bonds: B:R.300, B:V.381, B:W.382 Water bridges: B:S.38, B:R.300, B:R.300, B:W.382 pi-Stacking: B:W.382, B:W.382 pi-Cation interactions: B:W.382, B:W.382 H4B.11: 11 residues within 4Å: Chain C: S.38, M.40, R.300, V.381, W.382 Chain D: W.380, F.395, H.396, Q.397, E.398 Ligands: HEM.10 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.300, C:V.381, C:W.382 Water bridges: C:R.300, C:R.300, D:H.396 pi-Stacking: C:W.382, C:W.382 pi-Cation interactions: C:W.382 Hydrophobic interactions: D:E.398 H4B.17: 11 residues within 4Å: Chain C: W.380, F.395, H.396, Q.397, E.398 Chain D: S.38, M.40, R.300, V.381, W.382 Ligands: HEM.16 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:E.398 Water bridges: C:H.396, D:S.38, D:W.382 Hydrogen bonds: D:R.300, D:R.300, D:V.381, D:W.382 pi-Stacking: D:W.382, D:W.382

4 x EG8: N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}-3-(pyridin-3-yl)propan-1-amine(Non-covalent)

EG8.3: 10 residues within 4Å: Chain A: M.40, H.41, Q.182, P.269, A.270, V.271, G.290, E.296 Chain B: W.10 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:W.10 EG8.8: 10 residues within 4Å: Chain A: W.10 Chain B: M.40, H.41, Q.182, P.269, A.270, V.271, F.288, E.296 Ligands: HEM.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.182 pi-Stacking: B:F.288, A:W.10 EG8.12: 10 residues within 4Å: Chain C: M.40, H.41, Q.182, P.269, A.270, V.271, G.290, E.296 Chain D: W.10 Ligands: HEM.10 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C pi-Stacking: D:W.10 Hydrophobic interactions: C:Q.182 EG8.18: 11 residues within 4Å: Chain C: W.10 Chain D: M.40, H.41, Q.182, P.269, A.270, V.271, F.288, G.290, E.296 Ligands: HEM.16 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Q.182 pi-Stacking: C:W.10

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: K.110, S.126, L.128, Q.129, V.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.110, A:L.128, A:V.130, A:V.130 GOL.9: 6 residues within 4Å: Chain B: I.106, K.110, S.126, L.128, Q.129, V.130 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.110, B:S.126, B:L.128, B:V.130, B:V.130 GOL.13: 5 residues within 4Å: Chain C: I.106, K.110, L.128, Q.129, V.130 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.110, C:L.128, C:V.130, C:V.130 GOL.14: 3 residues within 4Å: Chain C: D.132, D.135, Y.145 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.132, C:Y.145 Water bridges: C:D.132 GOL.19: 5 residues within 4Å: Chain D: I.106, K.110, L.128, Q.129, V.130 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.110, D:L.128, D:V.130, D:V.130 Water bridges: D:Q.129

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: C.30, C.35, M.36 Chain B: C.30, C.35, M.36 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 ZN.15: 6 residues within 4Å: Chain C: C.30, C.35, M.36 Chain D: C.30, C.35, M.36 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Metal complexes: D:C.30, D:C.35, C:C.30, C:C.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mukherjee, P. et al., Novel 2,4-Disubstituted Pyrimidines as Potent, Selective, and Cell-Permeable Inhibitors of Neuronal Nitric Oxide Synthase. J.Med.Chem. (2015)

Release Date

2014-12-24

Peptides

NITRIC OXIDE SYNTHASE, BRAIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NITRIC OXIDE SYNTHASE, BRAIN

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