scPDB - 2pe2 entry

Protein Data Bank Entry:

PDB ID : 2pe2

Resolution :2.130 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:	24.240
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.748	509.625

% Hydrophobic	% Polar
46.36	53.64
According to VolSite

Ligand :

HET Code:	464
Formula:	C28H31N6O3
Molecular weight:	499.584 g/mol
DrugBank ID:	-
Buried Surface Area:	52.2 %
Polar Surface area:	133.88 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-3.71427	38.9091	44.8168

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
C6	CG1	VAL- 96	4.06	0	Hydrophobic	false
C7	CG2	VAL- 96	4.07	0	Hydrophobic	false
C9	CG2	VAL- 96	4.35	0	Hydrophobic	false
C6	CB	ALA- 109	4.43	0	Hydrophobic	false
C10	CB	ALA- 109	4.24	0	Hydrophobic	false
O17	NZ	LYS- 111	2.77	149.52	H-Bond (Protein Donor)	false
C10	CG1	VAL- 143	4.29	0	Hydrophobic	false
C9	CD1	LEU- 159	3.89	0	Hydrophobic	false
N1	O	SER- 160	2.79	177.25	H-Bond (Ligand Donor)	false
O3	N	ALA- 162	2.77	138.69	H-Bond (Protein Donor)	false
C41	CB	LYS- 169	3.59	0	Hydrophobic	false
C41	CE2	TYR- 170	4.42	0	Hydrophobic	false
N37	OH	TYR- 170	3.17	128.38	H-Bond (Ligand Donor)	false
C39	CD	LYS- 173	3.76	0	Hydrophobic	false
C10	CD1	LEU- 212	4.08	0	Hydrophobic	false
C6	CD1	LEU- 212	3.54	0	Hydrophobic	false
C9	CG2	THR- 222	4.04	0	Hydrophobic	false
N14	OD1	ASP- 223	3.39	146.18	H-Bond (Ligand Donor)	false