SMTL ID : 4d3t.1

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with N-{3-[(1S)-2-(3-{(Z)-[amino(thiophen-2-yl)methylidene]amino}phenoxy)-1-hydroxyethyl]phenyl}thiophene-2-carboximidamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: W.60, S.63, R.65, C.66, I.67, P.108, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: RFQ.3, GOL.5, POL.6 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:W.60, A:W.60, A:W.60, A:R.65, A:I.67, A:P.108, A:F.235, A:F.235, A:F.235, A:W.238, A:W.238, A:E.243, A:V.300, A:Y.355, A:Y.355 Salt bridges: A:R.65 pi-Stacking: A:W.60 Metal complexes: A:C.66 HEM.11: 19 residues within 4Å: Chain B: W.60, S.63, R.65, C.66, I.67, P.108, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: RFQ.13, GOL.15, POL.16 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:W.60, B:R.65, B:I.67, B:P.108, B:F.235, B:F.235, B:F.235, B:W.238, B:W.238, B:E.243, B:V.300, B:Y.355, B:Y.355 Salt bridges: B:R.65 pi-Stacking: B:W.60 Metal complexes: B:C.66

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: Q.129, Y.239, N.248 Ligands: POL.6 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: Q.129, Y.239, N.248 Ligands: POL.16 Ligand excluded by PLIP

2 x RFQ: N-{3-[(1S)-2-(3-{(Z)-[amino(thiophen-2-yl)methylidene]amino}phenoxy)-1-hydroxyethyl]phenyl}thiophene-2-carboximidamide(Non-covalent)

RFQ.3: 17 residues within 4Å: Chain A: H.128, P.216, I.218, F.235, N.236, G.237, W.238, Y.239, E.243, R.247, T.328, W.329 Chain B: W.327, F.342 Ligands: HEM.1, POL.6, GOL.19 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.216, A:I.218, A:I.218, A:F.235, A:W.329, B:W.327 Hydrogen bonds: A:H.128, A:W.238, A:E.243, A:R.247 pi-Stacking: A:W.329, B:F.342 RFQ.13: 17 residues within 4Å: Chain A: W.327, F.342 Chain B: H.128, P.216, I.218, F.235, N.236, G.237, W.238, Y.239, E.243, R.247, T.328, W.329 Ligands: GOL.9, HEM.11, POL.16 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.216, B:I.218, B:I.218, B:F.235, B:W.329, A:W.327 Hydrogen bonds: B:H.128, B:W.238, B:E.243, B:R.247 pi-Stacking: B:W.329, A:F.342

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: W.238, S.298, I.299, V.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.238, A:I.299 Water bridges: A:V.297, A:S.298 GOL.5: 6 residues within 4Å: Chain A: R.65, M.221, Y.355, F.356, Y.357 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.357 GOL.8: 2 residues within 4Å: Chain A: V.183, W.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.184 Water bridges: A:L.158, A:W.184 GOL.9: 5 residues within 4Å: Chain A: W.327, R.344, S.345 Chain B: T.328 Ligands: RFQ.13 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.344, B:T.328, B:T.328 GOL.10: 6 residues within 4Å: Chain A: Y.136, E.137, S.138, E.141, I.143, R.164 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.138, A:E.141, A:R.164, A:R.164 GOL.14: 4 residues within 4Å: Chain B: W.238, S.298, I.299, V.300 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.238, B:I.299 Water bridges: B:V.297, B:S.298 GOL.15: 6 residues within 4Å: Chain B: R.65, M.221, Y.355, F.356, Y.357 Ligands: HEM.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.357 GOL.18: 2 residues within 4Å: Chain B: V.183, W.184 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.184 Water bridges: B:L.158, B:W.184 GOL.19: 5 residues within 4Å: Chain A: T.328 Chain B: W.327, R.344, S.345 Ligands: RFQ.3 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.344, A:T.328, A:T.328 GOL.20: 6 residues within 4Å: Chain B: Y.136, E.137, S.138, E.141, I.143, R.164 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.138, B:E.141, B:R.164, B:R.164

4 x POL: N-PROPANOL(Non-covalent)

POL.6: 7 residues within 4Å: Chain A: E.243, R.247, N.248, R.254 Ligands: HEM.1, CL.2, RFQ.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.247 POL.7: 5 residues within 4Å: Chain A: G.144, D.166, R.254, Y.255, K.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.257, A:K.257 Water bridges: A:D.166 POL.16: 7 residues within 4Å: Chain B: E.243, R.247, N.248, R.254 Ligands: HEM.11, CL.12, RFQ.13 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.247 POL.17: 5 residues within 4Å: Chain B: G.144, D.166, R.254, Y.255, K.257 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.257, B:K.257 Water bridges: B:D.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holden, J.K. et al., Structure-Based Design of Bacterial Nitric Oxide Synthase Inhibitors. J.Med.Chem. (2015)

Release Date

2015-01-14

Peptides

NITRIC OXIDE SYNTHASE OXYGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NITRIC OXIDE SYNTHASE OXYGENASE

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