3ZCS | pdb_00003zcs

Rabbit muscle glycogen phosphorylase b in complex with N-(1-naphthoyl) -N-beta-D-glucopyranosyl urea determined at 2.07 A resolution

PDB DOI: https://doi.org/10.2210/pdb3ZCS/pdb

Classification: TRANSFERASE
Organism(s): Oryctolagus cuniculus
Mutation(s): Yes

Deposited: 2012-11-21 Released: 2013-12-11
Deposition Author(s): Chrysina, E.D., Nagy, V., Felfoldi, N., Konya, B., Telepo, K., Praly, J.P., Docsa, T., Gergely, P., Alexacou, K.M., Hayes, J.M., Konstantakaki, M., Kardakaris, R., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G., Somsak, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.217 (Depositor), 0.217 (DCC)
R-Value Work:
0.192 (Depositor), 0.191 (DCC)
R-Value Observed:
0.193 (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

Synthesis, Kinetic, Computational and Crystallographic Evaluation of N-Acyl-N-Beta-D- Glucopyranosyl)Ureas, Nanomolar Glucose Analogue Inhibitors of Glycogen Phosphorylase, Potential Antidiabetic Agents

Chrysina, E.D., Nagy, V., Felfoldi, N., Konya, B., Telepo, K., Praly, J.P., Docsa, T., Gergely, P., Alexacou, K.M., Hayes, J.M., Konstantakaki, M., Kardakaris, R., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G., Somsak, L.

To be published.

Macromolecule Content

Total Structure Weight: 98.39 kDa
Atom Count: 6,898
Modeled Residue Count: 807
Deposited Residue Count: 843
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOGEN PHOSPHORYLASE, MUSCLE FORM	A	843	Oryctolagus cuniculus	Mutation(s): 1 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAW Query on CAW 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]	N-[[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]carbamoyl]naphthalene-1-carboxamide C₁₈ H₂₀ N₂ O₇ VEHFJUDJKOIMSO-OWVAZHOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
IMP Query on IMP 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]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density 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] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
CAW	BindingDB: 3ZCS	Ki: min: 5000, max: 1.50e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.217 (Depositor), 0.217 (DCC)
R-Value Work: 0.192 (Depositor), 0.191 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.283	α = 90
b = 128.283	β = 90
c = 116.513	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-12-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-12-11
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Derived calculations
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description