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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:

1c8k

1.760 Å

X-ray

2000-05-11

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:24.040
Number of residues:27
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.645651.375

% Hydrophobic% Polar
51.3048.70
According to VolSite

Ligand :
1c8k_1 Structure
HET Code: CPB
Formula: C21H20ClNO5
Molecular weight: 401.840 g/mol
DrugBank ID: DB03496
Buried Surface Area:45.69 %
Polar Surface area: 94.26 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 4
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
39.37236.436229.7552


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
C14CE1PHE- 2854.020Hydrophobic
C13CZPHE- 2853.90Hydrophobic
C10CBPHE- 2854.310Hydrophobic
DuArDuArPHE- 2853.670Aromatic Face/Face
C25CD1ILE- 3803.590Hydrophobic
C25CGGLU- 3823.350Hydrophobic
CL1CZTYR- 6133.680Hydrophobic
C5CBTYR- 6133.650Hydrophobic
O4OHOH- 10352.62179.97H-Bond
(Protein Donor)
O5OHOH- 12093.16179.98H-Bond
(Protein Donor)