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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:

2phk

2.600 Å

X-ray

1998-06-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform
ID:PHKG1_RABIT
AC:P00518
Organism:Oryctolagus cuniculus
Reign:Eukaryota
TaxID:9986
EC Number:2.7.11.19


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:21.459
Number of residues:37
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.934577.125

% Hydrophobic% Polar
56.1443.86
According to VolSite

Ligand :
2phk_1 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:60.26 %
Polar Surface area: 319.88 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
47.963510.056348.5997


Binding mode :
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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
O1BOGSER- 313.03163.33H-Bond
(Protein Donor)
C1'CG1VAL- 3340Hydrophobic
C5'CG2VAL- 333.70Hydrophobic
O2BNZLYS- 483.220Ionic
(Protein Cationic)
O1ANZLYS- 483.210Ionic
(Protein Cationic)
O1ANZLYS- 483.21135.42H-Bond
(Protein Donor)
N6OASP- 1042.99170.42H-Bond
(Ligand Donor)
N1NMET- 1063.17163.87H-Bond
(Protein Donor)
C2'CGGLU- 1103.860Hydrophobic
O2'OE2GLU- 1102.54159.73H-Bond
(Ligand Donor)
O2GNZLYS- 1513.22148.78H-Bond
(Protein Donor)
O2GNZLYS- 1513.220Ionic
(Protein Cationic)
O3'OGLU- 1533.03155.43H-Bond
(Ligand Donor)
C2'CD2LEU- 15640Hydrophobic
O3GMN MN- 3822.260Metal Acceptor
O2BMN MN- 3822.260Metal Acceptor
O2GMN MN- 3832.020Metal Acceptor
O3BMN MN- 3832.710Metal Acceptor
O2AMN MN- 3832.130Metal Acceptor