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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:

4cb5

1.500 Å

X-ray

2013-10-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Polymerase basic protein 2
ID:Q2LG68_9INFA
AC:Q2LG68
Organism:Influenza A virus )
Reign:Viruses
TaxID:365107
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:14.242
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.428364.500

% Hydrophobic% Polar
56.4843.52
According to VolSite

Ligand :
4cb5_1 Structure
HET Code: 93G
Formula: C15H15N6O4
Molecular weight: 343.317 g/mol
DrugBank ID: -
Buried Surface Area:48.02 %
Polar Surface area: 156.67 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-50.0024.4756-3.13928


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
C1'CE1PHE- 3233.660Hydrophobic
CGCD1PHE- 3233.340Hydrophobic
CD1CBPHE- 3234.070Hydrophobic
CZCBPHE- 3233.90Hydrophobic
DuArDuArHIS- 3573.360Aromatic Face/Face
N1OE1GLU- 3612.66178.93H-Bond
(Ligand Donor)
N2OE2GLU- 3612.79173.11H-Bond
(Ligand Donor)
O6NZLYS- 3762.82163.8H-Bond
(Protein Donor)