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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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PDB Description
Binding Site
Binding Site Similarity
Cavity Similarity
Ligand
Binding Mode
Binding Mode Similarity
Protein Data Bank Entry:

2y7j

2.500 Å

X-ray

2011-01-31

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:7.4107.9008.2300.4008.2305
List of CHEMBLId :

CHEMBL535


Interactomes:
Interactome scPDB Proteins-Proteins
Interactome scPDB Proteins-Ligands
Interactome scPDB Ligands-Proteins
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Phosphorylase b kinase gamma catalytic chain, liver/testis isoform
ID:PHKG2_HUMAN
AC:P15735
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.19

Chains:

Chain Name:Percentage of Residues
within binding site
C100 %

Ligand binding site composition:

B-Factor:39.125
Number of residues:25
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.647644.625

% Hydrophobic% Polar
52.3647.64
According to VolSite

Ligand :
2y7j_3 Structure
HET Code: B49
Formula: C22H28FN4O2
Molecular weight: 399.482 g/mol
DrugBank ID: DB01268
Buried Surface Area:44.7 %
Polar Surface area: 78.43 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
-25.86079.02679-2.12703


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
C4CG2ILE- 304.240Hydrophobic
N25OILE- 302.89126.67H-Bond
(Ligand Donor)
C7CG1VAL- 383.970Hydrophobic
F29CG2VAL- 384.220Hydrophobic
F29CDLYS- 534.490Hydrophobic
C6CG1ILE- 913.690Hydrophobic
C5CD2PHE- 1073.450Hydrophobic
C6CBPHE- 1073.460Hydrophobic
N24OASP- 1082.73173.23H-Bond
(Ligand Donor)
O27NMET- 1102.73158.8H-Bond
(Protein Donor)
C3CGGLU- 1144.160Hydrophobic
C41CBASP- 1174.190Hydrophobic
C17CD1LEU- 1603.490Hydrophobic