scPDB - 4mpn entry

Protein Data Bank Entry:

PDB ID : 4mpn

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2013-09-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
A	100 %

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

Ligandability	Volume (Å3)
0.916	297.000

% Hydrophobic	% Polar
57.95	42.05
According to VolSite

Ligand :

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

X	Y	Z
14.3216	2.11318	-37.3138

Binding mode :

What is Poseview ?

2D View
3D View

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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C04	CB	ASN- 255	3.44	0	Hydrophobic	false
C17	CG	ARG- 258	3.96	0	Hydrophobic	false
C15	CB	ALA- 259	4.01	0	Hydrophobic	false
C12	CB	ALA- 259	3.42	0	Hydrophobic	false
O20	OE1	GLU- 262	2.73	158.13	H-Bond (Ligand Donor)	false
C16	CB	GLU- 262	4.14	0	Hydrophobic	false
O01	OD1	ASP- 290	3.39	127.53	H-Bond (Ligand Donor)	false
O01	OD2	ASP- 290	2.58	163.42	H-Bond (Ligand Donor)	false
C07	CD1	LEU- 303	3.89	0	Hydrophobic	false
C06	CD1	LEU- 330	4.24	0	Hydrophobic	false
C04	CD2	LEU- 346	4.28	0	Hydrophobic	false
C06	CD1	LEU- 346	4.09	0	Hydrophobic	false
C02	CB	THR- 354	3.68	0	Hydrophobic	false
C08	CG2	THR- 354	4.14	0	Hydrophobic	false
C03	CG2	THR- 354	3.93	0	Hydrophobic	false
O22	OG1	THR- 354	2.78	155.3	H-Bond (Protein Donor)	false
O22	O	HOH- 602	3.1	179.96	H-Bond (Protein Donor)	false