scPDB - 2r7b entry

Protein Data Bank Entry:

PDB ID : 2r7b

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2007-09-07

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:	35.684
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.856	533.250

% Hydrophobic	% Polar
45.57	54.43
According to VolSite

Ligand :

HET Code:	253
Formula:	C19H18N4O2
Molecular weight:	334.372 g/mol
DrugBank ID:	DB06932
Buried Surface Area:	54.72 %
Polar Surface area:	96.28 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
83.7744	16.0054	12.9593

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
C1	CD2	LEU- 88	4.43	0	Hydrophobic	false
C3	CD2	LEU- 88	4.34	0	Hydrophobic	false
C4	CD1	LEU- 88	4.43	0	Hydrophobic	false
C22	CB	LEU- 88	3.94	0	Hydrophobic	false
C12	CG1	VAL- 96	4.23	0	Hydrophobic	false
C17	CG2	VAL- 96	3.7	0	Hydrophobic	false
C15	CG2	VAL- 96	3.62	0	Hydrophobic	false
C8	CB	ALA- 109	3.81	0	Hydrophobic	false
C18	CD1	LEU- 159	4.17	0	Hydrophobic	false
N1	O	SER- 160	2.98	172.76	H-Bond (Ligand Donor)	false
C1	CE1	TYR- 161	3.77	0	Hydrophobic	false
N6	N	ALA- 162	2.91	155	H-Bond (Protein Donor)	false
C4	CB	ALA- 162	4.21	0	Hydrophobic	false
C25	CG	GLU- 166	3.78	0	Hydrophobic	false
C12	CD1	LEU- 212	4.47	0	Hydrophobic	false
C8	CD1	LEU- 212	3.51	0	Hydrophobic	false
N20	OG1	THR- 222	3.27	167.95	H-Bond (Protein Donor)	false
C17	CG2	THR- 222	4.43	0	Hydrophobic	false