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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:

3dxj

3.000 Å

X-ray

2008-07-24

Molecular Function:
Binding Site :

Uniprot Annotation

Name:DNA-directed RNA polymerase subunit betaDNA-directed RNA polymerase subunit beta'
ID:RPOB_THET8RPOC_THET8
AC:Q8RQE9Q8RQE8
Organism:Thermus thermophilus
Reign:Bacteria
TaxID:300852
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
M37 %
N63 %


Ligand binding site composition:

B-Factor:62.119
Number of residues:43
Including
Standard Amino Acids: 43
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.703985.500

% Hydrophobic% Polar
63.0136.99
According to VolSite

Ligand :
3dxj_2 Structure
HET Code: NE6
Formula: C23H31NO6
Molecular weight: 417.495 g/mol
DrugBank ID: DB08266
Buried Surface Area:55.24 %
Polar Surface area: 99.1 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 0
Rings: 1
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 11

Mass center Coordinates

XYZ
163.449-29.367746.307


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
C21CZPHE- 6143.490Hydrophobic
C22CZPHE- 6144.090Hydrophobic
C23CE1PHE- 6143.410Hydrophobic
C21CD2LEU- 6193.310Hydrophobic
C10CG2VAL- 10373.980Hydrophobic
C9CG2VAL- 10374.040Hydrophobic
O14NE1TRP- 10383.21125.96H-Bond
(Protein Donor)
C8CD2LEU- 10534.350Hydrophobic
C17CBSER- 10843.810Hydrophobic
C17CD2LEU- 10883.950Hydrophobic
C14CBVAL- 10994.480Hydrophobic
C14CBHIS- 11033.240Hydrophobic
C14CD1ILE- 12233.560Hydrophobic
C24CBALA- 14384.490Hydrophobic
C24CG2THR- 14433.770Hydrophobic
C14CBLYS- 14634.410Hydrophobic
C10CG1VAL- 14663.820Hydrophobic
C17CG1ILE- 14674.430Hydrophobic
C21CD1ILE- 14674.020Hydrophobic
C22CD1ILE- 14673.50Hydrophobic