scPDB - 2pe1 entry

Protein Data Bank Entry:

PDB ID : 2pe1

Resolution :2.140 Å

Experimental Method : X-ray

Deposition Date : 2007-04-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-phosphoinositide-dependent protein kinase 1
ID:	PDPK1_HUMAN
AC:	O15530
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	12.750
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.580	533.250

% Hydrophobic	% Polar
46.20	53.80
According to VolSite

Ligand :

HET Code:	517
Formula:	C15H14N4O2
Molecular weight:	282.297 g/mol
DrugBank ID:	DB07132
Buried Surface Area:	63.83 %
Polar Surface area:	100.34 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
-6.88324	43.8221	44.4145

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
C20	CB	LEU- 88	4.06	0	Hydrophobic	false
C7	CG1	VAL- 96	4.14	0	Hydrophobic	false
C8	CG2	VAL- 96	4.08	0	Hydrophobic	false
C10	CG2	VAL- 96	4.38	0	Hydrophobic	false
O15	NZ	LYS- 111	2.95	138.12	H-Bond (Protein Donor)	false
C11	CG1	VAL- 143	4.36	0	Hydrophobic	false
C11	CD1	LEU- 159	3.9	0	Hydrophobic	false
N1	O	SER- 160	2.98	173.5	H-Bond (Ligand Donor)	false
O4	N	ALA- 162	3.06	152.02	H-Bond (Protein Donor)	false
C11	CD1	LEU- 212	4.13	0	Hydrophobic	false
C7	CD1	LEU- 212	3.8	0	Hydrophobic	false
C11	CB	THR- 222	4.47	0	Hydrophobic	false
C10	CG2	THR- 222	4.03	0	Hydrophobic	false
N16	OD1	ASP- 223	3.25	142.82	H-Bond (Ligand Donor)	false