4D1P | pdb_00004d1p

Structure of human endothelial nitric oxide synthase heme domain IN COMPLEX WITH 6-((((3S, 5R)-5-(((6-AMINO-4-METHYLPYRIDIN-2-YL)METHOXY) METHYL)PYRROLIDIN-3-YL)OXY) METHYL)-4-METHYLPYRIDIN-2-AMINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 
    0.186 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structures of Human Constitutive Nitric Oxide Synthases

Li, H.Jamal, J.Plaza, C.Pineda, S.H.Chreifi, G.Jing, Q.Cinelli, M.A.Silverman, R.B.Poulos, T.L.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2667

  • DOI: https://doi.org/10.1107/S1399004714017064
  • Primary Citation Related Structures: 
    4D1N, 4D1O, 4D1P

  • PubMed Abstract: 

    Mammals produce three isoforms of nitric oxide synthase (NOS): neuronal NOS (nNOS), inducible NOS (iNOS) and endothelial NOS (eNOS). The overproduction of NO by nNOS is associated with a number of neurodegenerative disorders; therefore, a desirable therapeutic goal is the design of drugs that target nNOS but not the other isoforms. Crystallography, coupled with computational approaches and medicinal chemistry, has played a critical role in developing highly selective nNOS inhibitors that exhibit exceptional neuroprotective properties. For historic reasons, crystallography has focused on rat nNOS and bovine eNOS because these were available in high quality; thus, their structures have been used in structure-activity-relationship studies. Although these constitutive NOSs share more than 90% sequence identity across mammalian species for each NOS isoform, inhibitor-binding studies revealed that subtle differences near the heme active site in the same NOS isoform across species still impact enzyme-inhibitor interactions. Therefore, structures of the human constitutive NOSs are indispensible. Here, the first structure of human neuronal NOS at 2.03 Å resolution is reported and a different crystal form of human endothelial NOS is reported at 1.73 Å resolution.


  • Organizational Affiliation
    • Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences and Chemistry, University of California, Irvine, 517 Bison Avenue, Irvine, CA 92697-3900, USA.

Macromolecule Content 

  • Total Structure Weight: 102.67 kDa 
  • Atom Count: 7,449 
  • Modeled Residue Count: 803 
  • Deposited Residue Count: 880 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NITRIC OXIDE SYNTHASE, ENDOTHELIAL
A, B
440Homo sapiensMutation(s): 0 
EC: 1.14.13.39
UniProt & NIH Common Fund Data Resources
Find proteins for P29474 (Homo sapiens)
Explore P29474 
Go to UniProtKB:  P29474
PHAROS:  P29474
GTEx:  ENSG00000164867 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29474
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
C [auth A],
N [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Q16

Query on Q16



Download:Ideal Coordinates CCD File
E [auth A],
P [auth B]
6-((((3S, 5R)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine
C19 H27 N5 O2
NUKSCYDKRQJOFO-PBHICJAKSA-N
H4B

Query on H4B



Download:Ideal Coordinates CCD File
D [auth A],
O [auth B]
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
BTB

Query on BTB



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
R [auth B],
S [auth B]
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
GD

Query on GD



Download:Ideal Coordinates CCD File
L [auth A],
T [auth B]
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
K [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
M [auth B],
Q [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
Q16 BindingDB:  4D1P Ki: 6927 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free:  0.186 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.226α = 90
b = 110.378β = 90
c = 153.67γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description