6USN | pdb_00006usn

Co-crystal structure of SPR with compound 5

PDB DOI: https://doi.org/10.2210/pdb6USN/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-10-28 Released: 2019-12-11
Deposition Author(s): Huang, X., Wang, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free:
0.201 (Depositor), 0.208 (DCC)
R-Value Work:
0.168 (Depositor), 0.179 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Virtual screening to identify potent sepiapterin reductase inhibitors.

Gao, H., Schneider, S., Andrews, P., Wang, K., Huang, X., Sparling, B.A.

(2020) Bioorg Med Chem Lett 30: 126793-126793

PubMed: 31740247 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2019.126793
Primary Citation Related Structures:
6USN

PubMed Abstract:
Sepiapterin reductase has been identified as a potential drug target for neuropathic and inflammatory pain. Virtual screening was executed against a publicly available x-ray crystal structure of sepiapterin reductase. A set of structurally diverse and potent sepiapterin reductase inhibitors was identified. This set of compounds with favorable ligand efficiency and lipophilic efficiency are tractable for further optimization. An SAR follow-up library was synthesized based on one of the virtual screening hits exploring SAR.

Organizational Affiliation

Therapeutic Discovery, Amgen Inc., 360 Binney Street, Cambridge 02142, United States. Electronic address: hgao@amgen.com.

Macromolecule Content

Total Structure Weight: 119.7 kDa
Atom Count: 8,297
Modeled Residue Count: 1,032
Deposited Residue Count: 1,052
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sepiapterin reductase	A, B, C, D	263	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35270
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain O [auth B] SDF format, chain W [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain W [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain W [auth C]	DA [auth D], E [auth A], O [auth B], W [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain DA [auth D] Focus chain E [auth A] Focus chain O [auth B] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain E [auth A] Focus chain O [auth B] Focus chain W [auth C]
QGV (Subject of Investigation/LOI) Query on QGV Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain LA [auth D] SDF format, chain N [auth A] SDF format, chain V [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B]	CA [auth C], LA [auth D], N [auth A], V [auth B]	(2-hydroxyphenyl)[3-methyl-1-(pyridin-2-yl)-1H-pyrazolo[3,4-b]pyridin-5-yl]methanone C₁₉ H₁₄ N₄ O₂ LFBMVPHWBALPPW-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain LA [auth D] Focus chain N [auth A] Focus chain V [auth B] Interactions & Density Focus chain CA [auth C] Focus chain LA [auth D] Focus chain N [auth A] Focus chain V [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain M [auth A] SDF format, chain U [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B]	BA [auth C], M [auth A], U [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain M [auth A] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain M [auth A] Focus chain U [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain R [auth B] SDF format, chain P [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B]	EA [auth D] F [auth A] FA [auth D] G [auth A] GA [auth D] EA [auth D], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], JA [auth D], KA [auth D], P [auth B], Q [auth B], R [auth B], S [auth B], X [auth C], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain T [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B]	AA [auth C], J [auth A], K [auth A], L [auth A], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.201 (Depositor), 0.208 (DCC)
R-Value Work: 0.168 (Depositor), 0.179 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.286	α = 90
b = 146.286	β = 90
c = 179.505	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-12-11

Deposition Author(s):

Huang, X.

Wang, K.

Revision History (Full details and data files)

Version 1.0: 2019-12-11
Type: Initial release
Version 1.1: 2020-01-15
Changes: Database references
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description