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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:

4mpn

1.750 Å

X-ray

2013-09-13

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:15.361
Number of residues:27
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.916297.000

% Hydrophobic% Polar
57.9542.05
According to VolSite

Ligand :
4mpn_1 Structure
HET Code: PV0
Formula: C14H11NO6S
Molecular weight: 321.305 g/mol
DrugBank ID: -
Buried Surface Area:60.15 %
Polar Surface area: 132.34 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
14.32162.11318-37.3138


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
C04CBASN- 2553.440Hydrophobic
C17CGARG- 2583.960Hydrophobic
C15CBALA- 2594.010Hydrophobic
C12CBALA- 2593.420Hydrophobic
O20OE1GLU- 2622.73158.13H-Bond
(Ligand Donor)
C16CBGLU- 2624.140Hydrophobic
O01OD1ASP- 2903.39127.53H-Bond
(Ligand Donor)
O01OD2ASP- 2902.58163.42H-Bond
(Ligand Donor)
C07CD1LEU- 3033.890Hydrophobic
C06CD1LEU- 3304.240Hydrophobic
C04CD2LEU- 3464.280Hydrophobic
C06CD1LEU- 3464.090Hydrophobic
C02CBTHR- 3543.680Hydrophobic
C08CG2THR- 3544.140Hydrophobic
C03CG2THR- 3543.930Hydrophobic
O22OG1THR- 3542.78155.3H-Bond
(Protein Donor)
O22OHOH- 6023.1179.96H-Bond
(Protein Donor)