3DDS | pdb_00003dds

Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261

PDB DOI: https://doi.org/10.2210/pdb3DDS/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-06 Released: 2009-01-27
Deposition Author(s): Nolte, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.198 (Depositor), 0.205 (DCC)
R-Value Work:
0.174 (Depositor), 0.183 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Anthranilimide based glycogen phosphorylase inhibitors for the treatment of type 2 diabetes. Part 3: X-ray crystallographic characterization, core and urea optimization and in vivo efficacy.

Thomson, S.A., Banker, P., Bickett, D.M., Boucheron, J.A., Carter, H.L., Clancy, D.C., Cooper, J.P., Dickerson, S.H., Garrido, D.M., Nolte, R.T., Peat, A.J., Sheckler, L.R., Sparks, S.M., Tavares, F.X., Wang, L., Wang, T.Y., Weiel, J.E.

(2009) Bioorg Med Chem Lett 19: 1177-1182

PubMed: 19138846 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.12.085
Primary Citation Related Structures:
3DD1, 3DDS, 3DDW

PubMed Abstract:
Key binding interactions of the anthranilimide based glycogen phosphorylase a (GPa) inhibitor 2 from X-ray crystallography studies are described. This series of compounds bind to the AMP site of GP. Using the binding information the core and the phenyl urea moieties were optimized. This work culminated in the identification of compounds with single nanomolar potency as well as in vivo efficacy in a diabetic model.

Organizational Affiliation

Metabolic Center for Excellence in Drug Discovery, GlaxoSmithKline, 5 Moore Drive, PO Box 13398, Research Triangle Park, NC 27705, USA. stephen.a.thomson@gsk.com

Macromolecule Content

Total Structure Weight: 197.93 kDa
Atom Count: 14,698
Modeled Residue Count: 1,613
Deposited Residue Count: 1,696
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, liver form	A, B	848	Homo sapiens	Mutation(s): 0 Gene Names: PYGL EC: 2.4.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P06737 (Homo sapiens) Explore P06737 Go to UniProtKB: P06737
PHAROS: P06737 GTEx: ENSG00000100504
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06737
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
26B Query on 26B Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], M [auth B], N [auth B]	O-tert-butyl-N-[(3-{[(2,4,6-trimethylphenyl)carbamoyl]amino}naphthalen-2-yl)carbonyl]-L-threonine C₂₉ H₃₅ N₃ O₅ SIVVDUDKHBTSKI-CLOONOSVSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
NBG Query on NBG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	N-acetyl-beta-D-glucopyranosylamine C₈ H₁₅ N O₆ IBONACLSSOLHFU-JAJWTYFOSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
CFF Query on CFF Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B]	CAFFEINE C₈ H₁₀ N₄ O₂ RYYVLZVUVIJVGH-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
CFF	BindingDB: 3DDS	IC50: 6.48e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.198 (Depositor), 0.205 (DCC)
R-Value Work: 0.174 (Depositor), 0.183 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.403	α = 90
b = 124.403	β = 90
c = 123.614	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-01-27

Deposition Author(s):

Nolte, R.T.

Revision History (Full details and data files)

Version 1.0: 2009-01-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary