scPDB - 3qcq entry

Protein Data Bank Entry:

PDB ID : 3qcq

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2011-01-17

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:	35.845
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.919	448.875

% Hydrophobic	% Polar
54.89	45.11
According to VolSite

Ligand :

HET Code:	3Q0
Formula:	C13H15N7
Molecular weight:	269.305 g/mol
DrugBank ID:	-
Buried Surface Area:	68 %
Polar Surface area:	118.53 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
-43.2741	16.7098	12.0058

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
C13	CB	LEU- 88	4.31	0	Hydrophobic	false
C5	CG2	VAL- 96	3.5	0	Hydrophobic	false
C11	CG2	VAL- 96	3.93	0	Hydrophobic	false
C20	CG1	VAL- 96	4.19	0	Hydrophobic	false
C1	CG2	VAL- 96	3.59	0	Hydrophobic	false
C19	CB	ALA- 109	3.98	0	Hydrophobic	false
N10	NZ	LYS- 111	2.78	163.59	H-Bond (Protein Donor)	false
DuAr	NZ	LYS- 111	3.96	114.42	Pi/Cation	false
N9	OE2	GLU- 130	2.88	165.98	H-Bond (Ligand Donor)	false
C20	CD1	LEU- 159	4.03	0	Hydrophobic	false
N18	O	SER- 160	2.91	128.42	H-Bond (Ligand Donor)	false
N17	N	ALA- 162	3.01	175.61	H-Bond (Protein Donor)	false
N16	O	ALA- 162	3.22	134.38	H-Bond (Ligand Donor)	false
C14	CD1	LEU- 212	3.42	0	Hydrophobic	false
C19	CD1	LEU- 212	3.52	0	Hydrophobic	false
N7	OG1	THR- 222	2.78	146.58	H-Bond (Protein Donor)	false
C11	CG2	THR- 222	4.07	0	Hydrophobic	false