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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:

4fjl

1.870 Å

X-ray

2012-06-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:DNA-directed DNA polymerase
ID:DPOL_BPR69
AC:Q38087
Organism:Enterobacteria phage RB69
Reign:Viruses
TaxID:12353
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:20.727
Number of residues:30
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 3
Water Molecules: 0
Cofactors:
Metals: CA CA CA

Cavity properties

LigandabilityVolume (Å3)
0.5551164.375

% Hydrophobic% Polar
31.0168.99
According to VolSite

Ligand :
4fjl_1 Structure
HET Code: DGT
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB02181
Buried Surface Area:49.49 %
Polar Surface area: 315.33 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 3
Rings: 3
Aromatic rings: 1
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-1.24855-8.2620647.3442


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
O2GNSER- 4142.9178.34H-Bond
(Protein Donor)
O2BNALA- 4152.96174.1H-Bond
(Protein Donor)
C5'CBALA- 4154.030Hydrophobic
C4'CD1TYR- 4164.220Hydrophobic
C3'CGTYR- 4164.250Hydrophobic
C2'CD2TYR- 4163.620Hydrophobic
O3'NTYR- 4162.92176.04H-Bond
(Protein Donor)
O2GCZARG- 4823.760Ionic
(Protein Cationic)
O3GCZARG- 4823.650Ionic
(Protein Cationic)
O2GNH1ARG- 4822.91170.12H-Bond
(Protein Donor)
O3GNH2ARG- 4822.79166.23H-Bond
(Protein Donor)
O3GNZLYS- 5603.33166.13H-Bond
(Protein Donor)
O1ANZLYS- 5603.23153.38H-Bond
(Protein Donor)
O3GNZLYS- 5603.330Ionic
(Protein Cationic)
O1ANZLYS- 5603.230Ionic
(Protein Cationic)
O1BND2ASN- 5643.17153.72H-Bond
(Protein Donor)
C2'CBASN- 5644.230Hydrophobic
C4'CG2THR- 6224.060Hydrophobic
O1GCA CA- 10022.280Metal Acceptor
O2BCA CA- 10022.320Metal Acceptor
O2ACA CA- 10022.440Metal Acceptor
O2ACA CA- 10032.640Metal Acceptor