scPDB - 3qcy entry

Protein Data Bank Entry:

PDB ID : 3qcy

Resolution :2.200 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:	24.394
Number of residues:	39
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.673	492.750

% Hydrophobic	% Polar
51.37	48.63
According to VolSite

Ligand :

HET Code:	3Q3
Formula:	C22H22N8O2
Molecular weight:	430.462 g/mol
DrugBank ID:	-
Buried Surface Area:	61.04 %
Polar Surface area:	148.07 Å2

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

Mass center Coordinates

X	Y	Z
-45.4654	19.3403	11.3879

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
C4	CB	LEU- 88	4.19	0	Hydrophobic	false
O31	N	SER- 92	3.12	158.69	H-Bond (Protein Donor)	false
C7	CB	SER- 92	4.16	0	Hydrophobic	false
C9	CG2	VAL- 96	3.72	0	Hydrophobic	false
C4	CG1	VAL- 96	4.42	0	Hydrophobic	false
C11	CG2	VAL- 96	3.99	0	Hydrophobic	false
C8	CG1	VAL- 96	4.2	0	Hydrophobic	false
C12	CB	ALA- 109	3.88	0	Hydrophobic	false
N24	NZ	LYS- 111	3	171.71	H-Bond (Protein Donor)	false
C2	CB	TYR- 126	4.17	0	Hydrophobic	false
N29	OE2	GLU- 130	2.86	163.86	H-Bond (Ligand Donor)	false
C8	CD1	LEU- 159	4.12	0	Hydrophobic	false
N26	O	SER- 160	2.93	135.53	H-Bond (Ligand Donor)	false
N25	N	ALA- 162	2.95	176.42	H-Bond (Protein Donor)	false
N28	O	ALA- 162	3.24	128.27	H-Bond (Ligand Donor)	false
C10	CD1	LEU- 212	3.36	0	Hydrophobic	false
C12	CD1	LEU- 212	3.36	0	Hydrophobic	false
C9	CG2	THR- 222	4.39	0	Hydrophobic	false
C11	CG2	THR- 222	4.13	0	Hydrophobic	false
N23	OG1	THR- 222	2.94	151.75	H-Bond (Protein Donor)	false
N30	OD1	ASP- 223	2.75	147.09	H-Bond (Ligand Donor)	false
C2	CG2	THR- 226	3.35	0	Hydrophobic	false
O31	O	HOH- 415	2.71	165.4	H-Bond (Protein Donor)	false