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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:

2zdx

2.540 Å

X-ray

2007-11-30

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial
ID:PDK4_HUMAN
AC:Q16654
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:44.785
Number of residues:31
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.834425.250

% Hydrophobic% Polar
50.0050.00
According to VolSite

Ligand :
2zdx_1 Structure
HET Code: P4A
Formula: C17H16N2O3
Molecular weight: 296.321 g/mol
DrugBank ID: DB08356
Buried Surface Area:50.34 %
Polar Surface area: 78.37 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 3
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-26.106111.100513.392


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
C23CBASN- 2583.480Hydrophobic
C21CBALA- 2624.060Hydrophobic
C8CG1VAL- 2984.490Hydrophobic
C25CD1LEU- 3064.370Hydrophobic
C34CD2LEU- 3064.480Hydrophobic
C15CD2LEU- 3063.370Hydrophobic
C34CD1PHE- 3303.710Hydrophobic
C24CD2LEU- 3503.90Hydrophobic
C21CBTHR- 3583.840Hydrophobic
C22CG2THR- 3583.760Hydrophobic
N2OHOH- 5112.86159.7H-Bond
(Ligand Donor)