Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3t3i

2.650 Å

X-ray

2011-07-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glycogen phosphorylase, muscle form
ID:PYGM_RABIT
AC:P00489
Organism:Oryctolagus cuniculus
Reign:Eukaryota
TaxID:9986
EC Number:2.4.1.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:17.215
Number of residues:37
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.738533.250

% Hydrophobic% Polar
48.7351.27
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3t3iHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
3t3i_1 Structure
HET Code: GPW
Formula: C11H13F3N2O7
Molecular weight: 342.225 g/mol
DrugBank ID: -
Buried Surface Area:77.52 %
Polar Surface area: 139.56 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 5
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
34.435922.982228.5337
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3t3iRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
O2NLEU- 1363.19147.92H-Bond
(Protein Donor)
C1'CBLEU- 1364.10Hydrophobic
C6'CBLEU- 1364.470Hydrophobic
F2CD1LEU- 1363.760Hydrophobic
C6'CBLEU- 1394.180Hydrophobic
N3OD1ASP- 2832.73162.68H-Bond
(Ligand Donor)
F1CBASN- 2844.380Hydrophobic
O4NASN- 2842.94158.45H-Bond
(Protein Donor)
O2'ND2ASN- 2843.47158.05H-Bond
(Protein Donor)
F2CBASP- 3394.340Hydrophobic
C7CBHIS- 3774.220Hydrophobic
F1CG2THR- 3783.60Hydrophobic
F3CBTHR- 3783.490Hydrophobic
F1CBALA- 3833.620Hydrophobic
O4'ND2ASN- 4843.39125.91H-Bond
(Protein Donor)
O2'OE1GLU- 6723.12157.6H-Bond
(Ligand Donor)
O3'OE1GLU- 6722.68156.87H-Bond
(Ligand Donor)
O3'NSER- 6742.93167.89H-Bond
(Protein Donor)
C4'CBSER- 6744.310Hydrophobic
O3'NGLY- 6753.15145.68H-Bond
(Protein Donor)
O4'NGLY- 6752.84129.83H-Bond
(Protein Donor)