4XWY

Crystal structure of human sepiapterin reductase in complex with an N-acetylserotinin analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Reduction of Neuropathic and Inflammatory Pain through Inhibition of the Tetrahydrobiopterin Pathway.

Latremoliere, A.Latini, A.Andrews, N.Cronin, S.J.Fujita, M.Gorska, K.Hovius, R.Romero, C.Chuaiphichai, S.Painter, M.Miracca, G.Babaniyi, O.Remor, A.P.Duong, K.Riva, P.Barrett, L.B.Ferreiros, N.Naylor, A.Penninger, J.M.Tegeder, I.Zhong, J.Blagg, J.Channon, K.M.Johnsson, K.Costigan, M.Woolf, C.J.

(2015) Neuron 86: 1393-1406

  • DOI: https://doi.org/10.1016/j.neuron.2015.05.033
  • Primary Citation of Related Structures:  
    4XWY

  • PubMed Abstract: 

    Human genetic studies have revealed an association between GTP cyclohydrolase 1 polymorphisms, which decrease tetrahydrobiopterin (BH4) levels, and reduced pain in patients. We now show that excessive BH4 is produced in mice by both axotomized sensory neurons and macrophages infiltrating damaged nerves and inflamed tissue. Constitutive BH4 overproduction in sensory neurons increases pain sensitivity, whereas blocking BH4 production only in these cells reduces nerve injury-induced hypersensitivity without affecting nociceptive pain. To minimize risk of side effects, we targeted sepiapterin reductase (SPR), whose blockade allows minimal BH4 production through the BH4 salvage pathways. Using a structure-based design, we developed a potent SPR inhibitor and show that it reduces pain hypersensitivity effectively with a concomitant decrease in BH4 levels in target tissues, acting both on sensory neurons and macrophages, with no development of tolerance or adverse effects. Finally, we demonstrate that sepiapterin accumulation is a sensitive biomarker for SPR inhibition in vivo.


  • Organizational Affiliation

    Kirby Neurobiology Center, Boston Children's Hospital and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sepiapterin reductase
A, B, C, D
275Homo sapiensMutation(s): 0 
Gene Names: SPR
EC: 1.1.1.153
UniProt & NIH Common Fund Data Resources
Find proteins for P35270 (Homo sapiens)
Explore P35270 
Go to UniProtKB:  P35270
PHAROS:  P35270
GTEx:  ENSG00000116096 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35270
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
P [auth C],
S [auth D]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
43O
Query on 43O

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
Q [auth C],
T [auth D]
N-[2-(5-hydroxy-2-methyl-1H-indol-3-yl)ethyl]-2-methoxyacetamide
C14 H18 N2 O3
YBXBWBBVLXZQBJ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
M [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
O [auth B],
R [auth C],
U [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
43O Binding MOAD:  4XWY IC50: 54 (nM) from 1 assay(s)
BindingDB:  4XWY IC50: min: 11, max: 310 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.84α = 90
b = 144.84β = 90
c = 180.695γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
Cootmodel building
MOLREPphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Data collection
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description