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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

1zdg

2.300 Å

X-ray

2005-04-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glycogenin-1
ID:GLYG_RABIT
AC:P13280
Organism:Oryctolagus cuniculus
Reign:Eukaryota
TaxID:9986
EC Number:2.4.1.186


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:51.144
Number of residues:34
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: MN

Cavity properties

LigandabilityVolume (Å3)
0.104442.125

% Hydrophobic% Polar
40.4659.54
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median1zdgHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
1zdg_1 Structure
HET Code: UPG
Formula: C15H22N2O17P2
Molecular weight: 564.286 g/mol
DrugBank ID: DB01861
Buried Surface Area:59.43 %
Polar Surface area: 316.82 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 7
Rings: 3
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 9

Mass center Coordinates

XYZ
5.20061-37.002486.6142
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median1zdgRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation801020Highcharts.com


Binding mode :
What is Poseview ?
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C1CCD2LEU- 84.160Hydrophobic
O2COLEU- 82.67160.94H-Bond
(Ligand Donor)
N3OG1THR- 102.72134.8H-Bond
(Ligand Donor)
O2NTHR- 102.93137.13H-Bond
(Protein Donor)
C3CCE2TYR- 143.580Hydrophobic
C2CCD2TYR- 143.490Hydrophobic
C1CCG1VAL- 814.180Hydrophobic
O6'OD2ASP- 1013.1173.4H-Bond
(Ligand Donor)
C3CCBASP- 1014.360Hydrophobic
O2CNALA- 1023.02154.01H-Bond
(Protein Donor)
O3CNALA- 1022.89121.71H-Bond
(Protein Donor)
C2CCBALA- 1023.690Hydrophobic
O3COD1ASP- 1032.76129.66H-Bond
(Ligand Donor)
O3CNASP- 1033.41139.15H-Bond
(Protein Donor)
C4'CBGLN- 1634.460Hydrophobic
O4'NE2GLN- 1632.7124.62H-Bond
(Protein Donor)
C5'CD2LEU- 2133.890Hydrophobic
O1ANZLYS- 2173.730Ionic
(Protein Cationic)
O2ANZLYS- 2173.80Ionic
(Protein Cationic)
O2BNZLYS- 2172.910Ionic
(Protein Cationic)
O2BNZLYS- 2172.91139.36H-Bond
(Protein Donor)
O1AMN MN- 4002.50Metal Acceptor
O1BMN MN- 4001.90Metal Acceptor
O6'OHOH- 4402.71143.94H-Bond
(Protein Donor)