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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:

4cb6

1.900 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
B100 %


Ligand binding site composition:

B-Factor:27.986
Number of residues:27
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals: IOD

Cavity properties

LigandabilityVolume (Å3)
0.222475.875

% Hydrophobic% Polar
49.6550.35
According to VolSite

Ligand :
4cb6_2 Structure
HET Code: 29R
Formula: C16H22N5O5
Molecular weight: 364.376 g/mol
DrugBank ID: -
Buried Surface Area:45.03 %
Polar Surface area: 142.56 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 2
Rings: 2
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 11

Mass center Coordinates

XYZ
9.3416912.534813.1768


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
O37NSER- 3212.74123.73H-Bond
(Protein Donor)
C12CE2PHE- 3233.480Hydrophobic
C32CE1PHE- 3234.290Hydrophobic
C13CD2PHE- 3233.730Hydrophobic
C32CDARG- 3324.350Hydrophobic
C34CBARG- 3324.220Hydrophobic
DuArDuArHIS- 3573.690Aromatic Face/Face
N1OE1GLU- 3612.79177.6H-Bond
(Ligand Donor)
N2OE2GLU- 3612.75167.09H-Bond
(Ligand Donor)
C32CE2PHE- 3634.220Hydrophobic
O6NZLYS- 3763.12152.51H-Bond
(Protein Donor)
CM7CE1PHE- 4043.740Hydrophobic
CM7CGGLN- 4063.940Hydrophobic
CM7CEMET- 4314.270Hydrophobic