scPDB - 3qcx entry

Protein Data Bank Entry:

PDB ID : 3qcx

Resolution :2.300 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:	36.203
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.979	799.875

% Hydrophobic	% Polar
47.26	52.74
According to VolSite

Ligand :

HET Code:	3Q2
Formula:	C16H19N7O
Molecular weight:	325.368 g/mol
DrugBank ID:	-
Buried Surface Area:	60.88 %
Polar Surface area:	118.97 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-43.7549	17.635	12.0255

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	CB	LEU- 88	4.26	0	Hydrophobic	false
C4	CG2	VAL- 96	3.77	0	Hydrophobic	false
C16	CG2	VAL- 96	4	0	Hydrophobic	false
C1	CG1	VAL- 96	4.39	0	Hydrophobic	false
C6	CG2	VAL- 96	3.97	0	Hydrophobic	false
C3	CG1	VAL- 96	4.12	0	Hydrophobic	false
C7	CB	ALA- 109	3.89	0	Hydrophobic	false
N18	NZ	LYS- 111	2.97	164.54	H-Bond (Protein Donor)	false
N23	OE2	GLU- 130	2.82	169.86	H-Bond (Ligand Donor)	false
C3	CD1	LEU- 159	4.09	0	Hydrophobic	false
N20	O	SER- 160	2.96	137.55	H-Bond (Ligand Donor)	false
N19	N	ALA- 162	2.97	176.41	H-Bond (Protein Donor)	false
N22	O	ALA- 162	3.2	129.8	H-Bond (Ligand Donor)	false
C5	CD1	LEU- 212	3.47	0	Hydrophobic	false
C7	CD1	LEU- 212	3.53	0	Hydrophobic	false
C4	CG2	THR- 222	4.31	0	Hydrophobic	false
C6	CG2	THR- 222	3.99	0	Hydrophobic	false
N17	OG1	THR- 222	2.82	153.04	H-Bond (Protein Donor)	false