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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:

3q23

1.800 Å

X-ray

2010-12-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Virion DNA-directed RNA polymerase
ID:RPOLV_BPN4
AC:Q859P9
Organism:Enterobacteria phage N4
Reign:Viruses
TaxID:10752
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:17.468
Number of residues:30
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 3
Water Molecules: 1
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.001668.250

% Hydrophobic% Polar
38.8961.11
According to VolSite

Ligand :
3q23_1 Structure
HET Code: G2P
Formula: C11H14N5O13P3
Molecular weight: 517.176 g/mol
DrugBank ID: DB03532
Buried Surface Area:50.64 %
Polar Surface area: 326.33 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 4
Rings: 3
Aromatic rings: 1
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
12.1725-80.6617229.319


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
O4'NH2ARG- 4243.27144.91H-Bond
(Protein Donor)
O3GNTHR- 5622.8171.32H-Bond
(Protein Donor)
O1BNASN- 5633.06173.24H-Bond
(Protein Donor)
C5'CBASN- 5634.340Hydrophobic
O3'NGLY- 5642.76157.09H-Bond
(Protein Donor)
O2BOHTYR- 6122.63162.54H-Bond
(Protein Donor)
O2GNH2ARG- 6663.02158.05H-Bond
(Protein Donor)
O2GCZARG- 6663.930Ionic
(Protein Cationic)
O2GNZLYS- 6703.920Ionic
(Protein Cationic)
O6ND2ASN- 6713.16148.59H-Bond
(Protein Donor)
C2'CG2THR- 6743.880Hydrophobic
C2'CE1TYR- 6784.130Hydrophobic
O2'OHTYR- 6782.82175.23H-Bond
(Protein Donor)
C5'CBASP- 9514.010Hydrophobic
O2AMN MN- 11072.330Metal Acceptor
O1GMN MN- 11092.230Metal Acceptor
O1BMN MN- 11092.130Metal Acceptor
O2AMN MN- 11092.290Metal Acceptor
O2'OHOH- 11282.69152.06H-Bond
(Ligand Donor)