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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:

4mp7

1.800 Å

X-ray

2013-09-12

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:25.070
Number of residues:28
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.705317.250

% Hydrophobic% Polar
57.4542.55
According to VolSite

Ligand :
4mp7_1 Structure
HET Code: PFT
Formula: C15H13NO3
Molecular weight: 255.269 g/mol
DrugBank ID: -
Buried Surface Area:63.31 %
Polar Surface area: 60.77 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
13.89512.23779-37.3934


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
C18CBASN- 2553.360Hydrophobic
C16CGARG- 2583.660Hydrophobic
C9CBALA- 2594.320Hydrophobic
C7CBALA- 2593.540Hydrophobic
C17CBGLU- 2623.990Hydrophobic
O14OD2ASP- 2902.52156.88H-Bond
(Ligand Donor)
C10CD1LEU- 3034.110Hydrophobic
C15CD1LEU- 3304.450Hydrophobic
C15CD1LEU- 3464.180Hydrophobic
C18CD2LEU- 3464.170Hydrophobic
O6OG1THR- 3542.62157.01H-Bond
(Protein Donor)
C9CBTHR- 3543.550Hydrophobic
C10CG2THR- 3544.40Hydrophobic
C13CG2THR- 3543.830Hydrophobic