2FET | pdb_00002fet

Synthesis of C-D-Glycopyranosyl-Hydroquinones and-Benzoquinones. Inhibition of PTP1B. Inhibition of and binding to glycogen phosphorylase in the crystal

PDB DOI: https://doi.org/10.2210/pdb2FET/pdb

Classification: TRANSFERASE
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2005-12-16 Released: 2006-12-19
Deposition Author(s): Chrysina, E.D., Kosmopoulou, M.N., Leonidas, D.D., Oikonomakos, N.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.213 (Depositor)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

In the Search of Glycogen Phosphorylase Inhibitors: Synthesis of C-D-Glycopyranosylbenzo(hydro)quinones Inhibition of and Binding to Glycogen Phosphorylase in the Crystal

He, L., Zhang, Y.Z., Tanoh, M., Chen, G.-R., Praly, J.-P., Chrysina, E.D., Tiraidis, C., Kosmopoulou, M., Leonidas, D.D., Oikonomakos, N.G.

(2007) European J Org Chem 4: 596-606

DOI: https://doi.org/10.1002/ejoc.200600548

Macromolecule Content

Total Structure Weight: 97.81 kDa
Atom Count: 6,862
Modeled Residue Count: 807
Deposited Residue Count: 842
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	A	842	Oryctolagus cuniculus	Mutation(s): 0 EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus) Explore P00489 Go to UniProtKB: P00489
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00489
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H53 Query on H53 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(1S)-1,5-anhydro-1-(2,5-dihydroxyphenyl)-D-glucitol C₁₂ H₁₆ O₇ QRWWXASRKFWQRP-ZIQFBCGOSA-N		Interactions Focus chain C [auth A]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.213 (Depositor)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.188 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.308	α = 90
b = 128.308	β = 90
c = 116.046	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-12-19

Deposition Author(s):

Kosmopoulou, M.N.

Oikonomakos, N.G.

Revision History (Full details and data files)

Version 1.0: 2006-12-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.