9q55

Structure of human endothelial nitric oxide synthase heme domain bound with 6-((2,3-difluoro-5-(2-(4-fluoropiperidin-1-yl)ethyl)phenoxy)methyl)-4-methylpyridin-2-amine

Method: X-RAY DIFFRACTION Dmax: 143.2 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nitric oxide synthase 3

Homo sapiens

UniProt P29474

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 41–480 Chain B; UniProt 41–480 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 H4B 5,6,7,8-TETRAHYDROBIOPTERIN × 2 A1CN8 6-({2,3-difluoro-5-[2-(4-fluoropiperidin-1-yl)ethyl]phenoxy}methyl)-4-methylpyridin-2-amine × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 GOL GLYCEROL × 3 CL CHLORIDE ION × 2 ZN ZINC ION × 1 CA CALCIUM ION × 2 GD GADOLINIUM ATOM × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;277 K;10-12% PEG3350, 0.1M BIS-TRIS 0.2-0.3M MG ACETATE 0.1M GDCL3 10% GLYCEROL, 5 MM TCEP Resolution 2.10 Å R-free 0.229
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 41–480 Chain D; UniProt 41–480 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 H4B 5,6,7,8-TETRAHYDROBIOPTERIN × 2 A1CN8 6-({2,3-difluoro-5-[2-(4-fluoropiperidin-1-yl)ethyl]phenoxy}methyl)-4-methylpyridin-2-amine × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 GOL GLYCEROL × 3 CL CHLORIDE ION × 2 ZN ZINC ION × 1 GD GADOLINIUM ATOM × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;277 K;10-12% PEG3350, 0.1M BIS-TRIS 0.2-0.3M MG ACETATE 0.1M GDCL3 10% GLYCEROL, 5 MM TCEP Resolution 2.10 Å R-free 0.229

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

94 other PDB entries and 182 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOS3_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–440; UniProt 41–480 Author chain B; PDBConstruct 1–440; UniProt 41–480 Author chain C; PDBConstruct 1–440; UniProt 41–480 Author chain D; PDBConstruct 1–440; UniProt 41–480

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9q55

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9q55
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9q55
Deposition date deposition_date2025-08-20
Structure title titleStructure of human endothelial nitric oxide synthase heme domain bound with 6-((2,3-difluoro-5-(2-(4-fluoropiperidin-1-yl)ethyl)phenoxy)methyl)-4-methylpyridin-2-amine
Keywords keywordsnitric oxide synthase inhibitor binding, OXIDOREDUCTASE-INHIBITOR complex, OXIDOREDUCTASE; OXIDOREDUCTASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier43.12
Radius of gyration Rg (electron density) rg_electron42.79
Forward intensity I(0) i01026390000.00
Molecular weight molecular_weight175950.0 kDa
Excluded volume excluded_volume169950 ų
Envelope volume envelope_volume298810 ų
Hydration-shell volume shell_volume58083 ų
Envelope diameter envelope_diameter150.1
Shell Rg shell_rg47.73
Envelope Rg envelope_rg42.59
Shape Rg shape_rg42.80
Total Rg total_rg42.92
Total atoms total_atoms13290
Residues n_residues1604
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax143.2
Rg (real space) rg_real43.17
Rg uncertainty (real space) rg_real_error1.69
I(0) (real space) i0_real1.0260e+09
I(0) uncertainty (real space) i0_real_error1.7900e+07
Rg (reciprocal space) rg_reciprocal43.12
I(0) (reciprocal space) i0_reciprocal1026000000.0000
Solution quality estimate total_estimate0.8861
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.7
Skewness Skewness skewness0.279
Kurtosis Kurtosis kurtosis-0.610
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha132000000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.887; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.887

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

8. Citations (1)

9. Files and Curves (10)