6I6P

SEPIAPTERIN REDUCTASE IN COMPLEX WITH COMPOUND 3

• PDB DOI: https://doi.org/10.2210/pdb6I6P/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-15 Released: 2019-07-10 
• Deposition Author(s): Alen, J., Schade, M., Wagener, M., Blaesse, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.208 
• R-Value Work: 0.154 
• R-Value Observed: 0.157 

Literature

Fragment-Based Discovery of Novel Potent Sepiapterin Reductase Inhibitors.

Alen, J., Schade, M., Wagener, M., Christian, F., Nordhoff, S., Merla, B., Dunkern, T.R., Bahrenberg, G., Ratcliffe, P.

(2019) J Med Chem 62: 6391-6397

• PubMed: 31244106 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b00218
• Primary Citation of Related Structures:  
  6I6C, 6I6F, 6I6P, 6I6T, 6I6V, 6I79


• PubMed Abstract: 
  

  Genome-wide-association studies in chronic low back pain patients identified sepiapterin reductase as a high interest target for developing new analgesics. Here we used ¹⁹ F NMR fragment screening for the discovery of novel, ligand-efficient SPR inhibitors. We report the crystal structures of six chemically diverse inhibitors complexed with SPR, identifying relevant interactions and binding modes in the sepiapterin pocket. Exploration of our initial fragment screening hit led to double-digit nanomolar inhibitors of SPR with excellent ligand efficiency.

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Organizational Affiliation: 

Grünenthal GmbH , Zieglerstraße 6 , 52078 Aachen , Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.17 kDa 
• Atom Count: 4,709 
• Modelled Residue Count: 528 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sepiapterin reductase	A, B	276	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
H4T	D [auth A], G [auth B]	6-azaspiro[3.4]octan-6-yl-[2,4-bis(chloranyl)-6-oxidanyl-phenyl]methanone C14 H15 Cl2 N O2 DGXBFJCZWBOKKO-UHFFFAOYSA-N
EDO	E [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
H4T	Binding MOAD:  6I6P	IC50: 580 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.208 
• R-Value Work: 0.154 
• R-Value Observed: 0.157 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.529	α = 90
b = 77.708	β = 90
c = 59.626	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Alen, J., Schade, M., Wagener, M., Blaesse, M.

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2019-07-24
  Changes: Data collection, Database references