4LUW

Structure of bovine endothelial nitric oxide synthase heme domain in complex with 6-((((3R,5S)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine

PDB DOI: https://doi.org/10.2210/pdb4LUW/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Bos taurus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-07-25 Released: 2013-10-23
Deposition Author(s): Li, H., Poulos, T.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.233
R-Value Work: 0.185
R-Value Observed: 0.187

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Structural and biological studies on bacterial nitric oxide synthase inhibitors.

Holden, J.K., Li, H., Jing, Q., Kang, S., Richo, J., Silverman, R.B., Poulos, T.L.

(2013) Proc Natl Acad Sci U S A 110: 18127-18131

PubMed: 24145412 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.1314080110
Primary Citation of Related Structures:
4LUW, 4LUX, 4LWA, 4LWB

PubMed Abstract:
Nitric oxide (NO) produced by bacterial NOS functions as a cytoprotective agent against oxidative stress in Staphylococcus aureus, Bacillus anthracis, and Bacillus subtilis. The screening of several NOS-selective inhibitors uncovered two inhibitors with potential antimicrobial properties. These two compounds impede the growth of B. subtilis under oxidative stress, and crystal structures show that each compound exhibits a unique binding mode. Both compounds serve as excellent leads for the future development of antimicrobials against bacterial NOS-containing bacteria.

Organizational Affiliation

Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, CA 92697-3900.

Macromolecule Content

Total Structure Weight: 102.06 kDa
Atom Count: 6,941
Modelled Residue Count: 809
Deposited Residue Count: 884
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitric oxide synthase, endothelial	A, B	442	Bos taurus	Mutation(s): 0 Gene Names: NOS3 EC: 1.14.13.39
UniProt
Find proteins for P29473 (Bos taurus) Explore P29473 Go to UniProtKB: P29473
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29473
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain J [auth B]
QJ8 Query on QJ8 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	6-({[(3R,5S)-5-{[(6-amino-4-methylpyridin-2-yl)methoxy]methyl}pyrrolidin-3-yl]oxy}methyl)-4-methylpyridin-2-amine C₁₉ H₂₇ N₅ O₂ NUKSCYDKRQJOFO-WMLDXEAASA-N		Interactions Focus chain E [auth A] Focus chain L [auth B]
H4B Query on H4B Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	5,6,7,8-TETRAHYDROBIOPTERIN C₉ H₁₅ N₅ O₃ FNKQXYHWGSIFBK-RPDRRWSUSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B]	H [auth A], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	F [auth A], G [auth A], M [auth B], N [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS Query on CAS	A, B	L-PEPTIDE LINKING	C₅ H₁₂ As N O₂ S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
QJ8	BindingDB: 4LUW	Ki: min: 2179, max: 2179 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.233
R-Value Work: 0.185
R-Value Observed: 0.187
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.114	α = 90
b = 106.557	β = 90
c = 156.852	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-10-23

Deposition Author(s):

Li, H.

Poulos, T.L.

Revision History (Full details and data files)

Version 1.0: 2013-10-23
Type: Initial release
Version 1.1: 2013-10-30
Changes: Database references
Version 1.2: 2013-11-06
Changes: Database references
Version 1.3: 2013-11-20
Changes: Database references
Version 1.4: 2017-11-15
Changes: Refinement description
Version 1.5: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.6: 2024-10-16
Changes: Structure summary