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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:

2bu2

2.400 Å

X-ray

2005-06-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
ID:PDK2_HUMAN
AC:Q15119
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.2


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:60.101
Number of residues:25
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.897239.625

% Hydrophobic% Polar
61.9738.03
According to VolSite

Ligand :
2bu2_1 Structure
HET Code: TF1
Formula: C18H20F3N3O3
Molecular weight: 383.365 g/mol
DrugBank ID: DB08608
Buried Surface Area:56.16 %
Polar Surface area: 84.64 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 1
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
56.961961.087378.7299


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
C6CD1LEU- 233.560Hydrophobic
F3CD1LEU- 233.90Hydrophobic
C14CD2LEU- 233.770Hydrophobic
C6CBGLN- 273.90Hydrophobic
C6CD2PHE- 283.890Hydrophobic
F1CE2PHE- 283.370Hydrophobic
C10CE1PHE- 313.640Hydrophobic
C10CG2THR- 404.150Hydrophobic
O2OGSER- 412.63163.76H-Bond
(Protein Donor)
C4CBSER- 414.40Hydrophobic
C10CBPHE- 443.870Hydrophobic
F3CE2PHE- 443.630Hydrophobic
F2CD2LEU- 453.290Hydrophobic
F2CBLEU- 1603.910Hydrophobic
F3CD2LEU- 1603.480Hydrophobic
C9CBGLN- 1633.840Hydrophobic
F1CBGLN- 1633.210Hydrophobic
F2CBHIS- 1644.250Hydrophobic
C9CD1ILE- 1674.330Hydrophobic
O1OHOH- 20912.54166.86H-Bond
(Protein Donor)