[English] 日本語
Yorodumi
- PDB-9cwi: Structure of human endothelial nitric oxide synthase heme domain ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cwi
TitleStructure of human endothelial nitric oxide synthase heme domain bound with 6-(5-((3,3-difluoroazetidin-1-yl)methyl)-2,3-difluorophenyl)-4-methylpyridin-2-amine dihydrochloride
ComponentsNitric oxide synthase, endothelial
KeywordsOXIDOREDUCTASE/INHIBITOR / nitric oxide synthase inhibitor binding / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of muscle hyperplasia / regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / 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 ...negative regulation of muscle hyperplasia / regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / 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 / positive regulation of guanylate cyclase activity / 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 potassium ion transport / negative regulation of calcium ion transport / nitric oxide mediated signal transduction / negative regulation of platelet activation / actin monomer binding / blood vessel remodeling / nitric-oxide synthase (NADPH) / 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 / eNOS activation / nitric oxide metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / negative regulation of blood pressure / homeostasis of number of cells within a tissue / response to hormone / nitric oxide biosynthetic process / removal of superoxide radicals / cell redox homeostasis / lipopolysaccharide-mediated signaling pathway / blood vessel diameter maintenance / VEGFR2 mediated vascular permeability / mitochondrion organization / establishment of localization in cell / negative regulation of smooth muscle cell proliferation / lung development / potassium ion transport / caveola / regulation of blood pressure / positive regulation of angiogenesis / calcium ion transport / vasodilation / endocytic vesicle membrane / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to heat / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / scaffold protein binding / angiogenesis / response to lipopolysaccharide / in utero embryonic development / cytoskeleton / Extra-nuclear estrogen signaling / calmodulin binding / Golgi membrane / negative regulation of cell population proliferation / heme binding / positive regulation of gene expression / Golgi apparatus / nucleus / plasma membrane / cytosol / cytoplasm
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 ION / 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: 1.73 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: Bioorg.Med.Chem. / Year: 2025
Title: Truncated pyridinylbenzylamines: Potent, selective, and highly membrane permeable inhibitors of human neuronal nitric oxide synthase.
Authors: Vasu, D. / Do, H.T. / Li, H. / Hardy, C.D. / Poulos, T.L. / Silverman, R.B.
History
DepositionJul 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)206,03046
Polymers197,3834
Non-polymers8,64742
Water17,781987
1
A: Nitric oxide synthase, endothelial
B: Nitric oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,38225
Polymers98,6922
Non-polymers4,69023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11430 Å2
ΔGint-156 kcal/mol
Surface area33200 Å2
MethodPISA
2
C: Nitric oxide synthase, endothelial
D: Nitric oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,64921
Polymers98,6922
Non-polymers3,95719
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-154 kcal/mol
Surface area33380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.431, 152.819, 108.317
Angle α, β, γ (deg.)90.00, 90.76, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 49345.770 Da / Num. of mol.: 4 / Fragment: heme domain
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)

-
Non-polymers , 9 types, 1029 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: isolated from a natural source / 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 / Comment: neurotransmitter*YM
#4: Chemical
ChemComp-A1A0D / (6M)-6-{5-[(3,3-difluoroazetidin-1-yl)methyl]-2,3-difluorophenyl}-4-methylpyridin-2-amine


Mass: 325.304 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H15F4N3 / 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.: 10 / 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.: 10 / 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-GD3 / GADOLINIUM ION


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 987 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.3 % / Description: rods
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10-12% PEG3350, 0.1M Bis-Tris, 0.2-0.3M Magnesium Acetate, 0.1M GdCl3, 10% Glycerol, 5 mM TCEP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2022 / 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: 1.73→49.07 Å / Num. obs: 197817 / % possible obs: 98.6 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.041 / Rrim(I) all: 0.09 / Χ2: 0.98 / Net I/σ(I): 10.4 / Num. measured all: 927245
Reflection shellResolution: 1.73→1.76 Å / % possible obs: 91.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 2.122 / Num. measured all: 38177 / Num. unique obs: 9145 / CC1/2: 0.322 / Rpim(I) all: 1.15 / Rrim(I) all: 2.424 / Χ2: 0.95 / Net I/σ(I) obs: 0.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.73→49.07 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 19735 5.03 %random
Rwork0.194 ---
obs0.1954 197735 98.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12815 0 542 987 14344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713765
X-RAY DIFFRACTIONf_angle_d1.15918819
X-RAY DIFFRACTIONf_dihedral_angle_d16.8375016
X-RAY DIFFRACTIONf_chiral_restr0.0551952
X-RAY DIFFRACTIONf_plane_restr0.0082409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.750.38366360.355911575X-RAY DIFFRACTION91
1.75-1.770.38386030.347511726X-RAY DIFFRACTION94
1.77-1.790.31896310.327711996X-RAY DIFFRACTION95
1.79-1.810.35916660.318612131X-RAY DIFFRACTION97
1.81-1.840.33526460.320512358X-RAY DIFFRACTION98
1.84-1.860.33216990.306912198X-RAY DIFFRACTION97
1.86-1.890.32795880.306112399X-RAY DIFFRACTION99
1.89-1.920.32986090.300812538X-RAY DIFFRACTION98
1.92-1.950.29976420.288712454X-RAY DIFFRACTION99
1.95-1.980.31296430.282112626X-RAY DIFFRACTION99
1.98-2.010.31846760.270912481X-RAY DIFFRACTION100
2.01-2.050.27156980.25512636X-RAY DIFFRACTION100
2.05-2.090.29547470.252912282X-RAY DIFFRACTION100
2.09-2.130.27377170.249712680X-RAY DIFFRACTION100
2.13-2.180.28696390.246112496X-RAY DIFFRACTION99
2.18-2.230.25866900.22812551X-RAY DIFFRACTION100
2.23-2.290.24826090.216712697X-RAY DIFFRACTION100
2.29-2.350.25116990.206212470X-RAY DIFFRACTION100
2.35-2.420.22456530.199112583X-RAY DIFFRACTION100
2.42-2.50.23777110.198212608X-RAY DIFFRACTION100
2.5-2.580.22686430.190812586X-RAY DIFFRACTION100
2.58-2.690.20597380.186212464X-RAY DIFFRACTION100
2.69-2.810.21746290.192312604X-RAY DIFFRACTION100
2.81-2.960.20226780.190812539X-RAY DIFFRACTION100
2.96-3.140.21035800.179812613X-RAY DIFFRACTION99
3.14-3.390.22616700.1812525X-RAY DIFFRACTION100
3.39-3.730.1966950.159912545X-RAY DIFFRACTION99
3.73-4.270.16236490.143712448X-RAY DIFFRACTION99
4.27-5.370.1776340.138712384X-RAY DIFFRACTION98
5.37-49.070.19546170.188612416X-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)
10.8130.3612-0.46312.0853-0.50311.96270.20620.39020.35520.02420.20420.3888-0.6132-0.5973-0.24420.38640.19710.12750.47530.22770.427764.006631.7744-184.6816
21.0294-0.2086-0.37951.223-0.54652.35410.0686-0.0380.04970.23990.05450.015-0.1255-0.12-0.12230.1959-0.0481-0.01590.17280.01410.233773.8138.488-156.9045
30.8881-0.20470.62041.8894-0.24952.05920.1664-0.2941-0.34690.07280.07270.23050.6106-0.292-0.15870.3809-0.0333-0.05840.31110.130.369192.768-34.2709-194.5925
40.99170.24650.43470.7202-0.08832.3834-0.03410.0326-0.045-0.06810.0573-0.0337-0.0670.1585-0.03080.22420.0434-0.00520.2021-0.00220.2674102.8639-10.3585-221.6621
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more