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- PDB-9q51: Structure of human endothelial nitric oxide synthase heme domain ... -

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Basic information

Entry
Database: PDB / ID: 9q51
TitleStructure of human endothelial nitric oxide synthase heme domain bound with 6-((5-(2-(diethylamino)ethyl)-2,3-difluorophenxy)methyl)-4-methylpyridin-2-amine
ComponentsNitric oxide synthase 3
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / nitric oxide synthase inhibitor binding / OXIDOREDUCTASE-INHIBITOR complex / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / negative regulation of muscle hyperplasia / tetrahydrobiopterin metabolic process / NOSTRIN mediated eNOS trafficking / smooth muscle hyperplasia / regulation of nervous system process / superoxide-generating NAD(P)H oxidase activity / ovulation from ovarian follicle / pulmonary valve morphogenesis ...regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / negative regulation of muscle hyperplasia / tetrahydrobiopterin metabolic process / NOSTRIN mediated eNOS trafficking / smooth muscle hyperplasia / regulation of nervous system process / superoxide-generating NAD(P)H oxidase activity / ovulation from ovarian follicle / pulmonary valve morphogenesis / response to fluid shear stress / negative regulation of biomineral tissue development / Nitric oxide stimulates guanylate cyclase / regulation of systemic arterial blood pressure by endothelin / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / arginine binding / aortic valve morphogenesis / endocardial cushion morphogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / cadmium ion binding / negative regulation of calcium ion transport / negative regulation of potassium ion transport / negative regulation of platelet activation / actin monomer binding / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / blood vessel remodeling / positive regulation of blood vessel endothelial cell migration / nitric-oxide synthase activity / endothelial cell migration / L-arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of sodium ion transport / negative regulation of blood pressure / response to hormone / nitric oxide metabolic process / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / nitric oxide biosynthetic process / homeostasis of number of cells within a tissue / removal of superoxide radicals / lung development / cell redox homeostasis / lipopolysaccharide-mediated signaling pathway / blood vessel diameter maintenance / VEGFR2 mediated vascular permeability / mitochondrion organization / negative regulation of smooth muscle cell proliferation / establishment of localization in cell / caveola / potassium ion transport / regulation of blood pressure / vasodilation / positive regulation of angiogenesis / endocytic vesicle membrane / calcium ion transport / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to heat / scaffold protein binding / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / angiogenesis / response to lipopolysaccharide / in utero embryonic development / cytoskeleton / calmodulin binding / Extra-nuclear estrogen signaling / Golgi membrane / negative regulation of cell population proliferation / heme binding / positive regulation of gene expression / Golgi apparatus / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding ...Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily
Similarity search - Domain/homology
: / GADOLINIUM ATOM / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsLi, H. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131920 United States
CitationJournal: To Be Published
Title: Highly potent, selective, and membrane permeable ether linked 2-aminopyridine-based human neuronal nitric oxide synthase inhibitors
Authors: Ansari, A. / Chrzanowski, R.T. / Li, H. / Hardy, C.D. / Poulos, T.L. / Silverman, R.B.
History
DepositionAug 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitric oxide synthase 3
B: Nitric oxide synthase 3
C: Nitric oxide synthase 3
D: Nitric oxide synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,56443
Polymers197,3834
Non-polymers8,18139
Water20,8071155
1
A: Nitric oxide synthase 3
B: Nitric oxide synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,80222
Polymers98,6922
Non-polymers4,11120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13360 Å2
ΔGint-157 kcal/mol
Surface area33080 Å2
MethodPISA
2
C: Nitric oxide synthase 3
D: Nitric oxide synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,76221
Polymers98,6922
Non-polymers4,07019
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12700 Å2
ΔGint-156 kcal/mol
Surface area32350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.990, 153.180, 108.591
Angle α, β, γ (deg.)90.00, 90.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Nitric oxide synthase 3 / Constitutive NOS / cNOS / EC-NOS / NOS type III / NOSIII / Nitric oxide synthase / endothelial / ...Constitutive NOS / cNOS / EC-NOS / NOS type III / NOSIII / Nitric oxide synthase / endothelial / Endothelial NOS / eNOS


Mass: 49345.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: endothelial / Gene: NOS3 / Plasmid: pCWori / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29474, nitric-oxide synthase (NADPH)

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Non-polymers , 10 types, 1194 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N5O3
#4: Chemical
ChemComp-A1COA / 6-({5-[2-(diethylamino)ethyl]-2,3-difluorophenoxy}methyl)-4-methylpyridin-2-amine


Mass: 349.418 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H25F2N3O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Gd
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1155 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.3 % / Description: rods
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10-12% PEG3350, 0.1M BIS-TRIS 0.2-0.3M MG ACETATE 0.1M GDCL3 10% GLYCEROL, 5 MM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2024 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.225 Å / Num. obs: 178506 / % possible obs: 98.8 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.053 / Rrim(I) all: 0.117 / Net I/σ(I): 8.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5 % / Rmerge(I) obs: 1.622 / Num. unique obs: 8843 / CC1/2: 0.393 / Rpim(I) all: 0.811 / Rrim(I) all: 1.82 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→47.225 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 17818 5.03 %random
Rwork0.19 ---
obs0.1919 178425 98.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12833 0 511 1155 14499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113793
X-RAY DIFFRACTIONf_angle_d0.97618774
X-RAY DIFFRACTIONf_dihedral_angle_d15.1078027
X-RAY DIFFRACTIONf_chiral_restr0.0531942
X-RAY DIFFRACTIONf_plane_restr0.0062410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.36335880.313511331X-RAY DIFFRACTION99
1.8205-1.84190.336150.306711042X-RAY DIFFRACTION99
1.8419-1.86430.3335910.312111262X-RAY DIFFRACTION98
1.8643-1.88790.34616300.304811113X-RAY DIFFRACTION99
1.8879-1.91280.32625220.295611277X-RAY DIFFRACTION99
1.9128-1.9390.35365810.299211251X-RAY DIFFRACTION99
1.939-1.96670.31245980.288811095X-RAY DIFFRACTION99
1.9667-1.9960.33345370.275111287X-RAY DIFFRACTION99
1.996-2.02720.29246110.260811145X-RAY DIFFRACTION99
2.0272-2.06050.26826340.247411186X-RAY DIFFRACTION99
2.0605-2.0960.29626590.25610786X-RAY DIFFRACTION96
2.096-2.13410.26436510.240511155X-RAY DIFFRACTION98
2.1341-2.17520.26155790.22911161X-RAY DIFFRACTION99
2.1752-2.21960.25725810.223411352X-RAY DIFFRACTION99
2.2196-2.26780.27995950.22811166X-RAY DIFFRACTION99
2.2678-2.32060.2475790.214311313X-RAY DIFFRACTION99
2.3206-2.37860.24625770.204311194X-RAY DIFFRACTION99
2.3786-2.44290.26846040.205611278X-RAY DIFFRACTION100
2.4429-2.51480.23086460.196511301X-RAY DIFFRACTION99
2.5148-2.5960.21385700.181411299X-RAY DIFFRACTION99
2.596-2.68870.22726570.183610902X-RAY DIFFRACTION97
2.6887-2.79640.23555840.182111105X-RAY DIFFRACTION98
2.7964-2.92360.22476200.182511297X-RAY DIFFRACTION100
2.9236-3.07770.24345170.183711413X-RAY DIFFRACTION100
3.0777-3.27050.22925670.180611311X-RAY DIFFRACTION100
3.2705-3.5230.20496310.162711323X-RAY DIFFRACTION99
3.523-3.87730.20025620.151111125X-RAY DIFFRACTION98
3.8773-4.4380.16226030.137511152X-RAY DIFFRACTION98
4.438-5.590.17115910.138311334X-RAY DIFFRACTION100
5.59-47.2250.19575380.181511203X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5458-0.08850.33641.326-0.01741.35740.12190.2174-0.1276-0.197-0.0064-0.0970.52160.1685-0.04030.47780.0296-0.03940.2404-0.07050.269-30.2-38.8623-76.4545
20.7448-0.18980.10440.70480.0161.75480.0012-0.0493-0.03520.03510.07370.0567-0.0142-0.0911-0.06190.1186-0.0283-0.00320.11210.00970.1681-40.5785-15.3273-49.3287
30.6061-0.1846-0.24921.41240.43411.36860.1488-0.28830.21860.00750.1286-0.2909-0.40140.3479-0.10870.3267-0.10780.0810.3422-0.14910.3333-1.123526.6416-86.3358
40.87420.1773-0.13651.05270.66571.87660.03750.04230.0151-0.16930.0965-0.0639-0.07790.0998-0.09250.16370.0309-0.00070.1577-0.00850.2027-11.16093.5609-114.0998
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 68:480)
2X-RAY DIFFRACTION2(chain B and resid 67:480)
3X-RAY DIFFRACTION3(chain C and resid 68:480)
4X-RAY DIFFRACTION4(chain D and resid 67:480)

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