scPDB - 1oky entry

Protein Data Bank Entry:

PDB ID : 1oky

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2003-08-01

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:	28.323
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.147	459.000

% Hydrophobic	% Polar
54.41	45.59
According to VolSite

Ligand :

HET Code:	STU
Formula:	C28H27N4O3
Molecular weight:	467.539 g/mol
DrugBank ID:	DB02010
Buried Surface Area:	65.81 %
Polar Surface area:	74.03 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	8
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
82.9175	17.7552	12.3376

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
C19	CB	LEU- 88	4.28	0	Hydrophobic	false
C3	CD2	LEU- 88	4.34	0	Hydrophobic	false
C4	CD1	LEU- 88	3.85	0	Hydrophobic	false
C6	CD1	LEU- 88	4.11	0	Hydrophobic	false
C20	CB	LEU- 88	3.77	0	Hydrophobic	false
C18	CG2	VAL- 96	4.09	0	Hydrophobic	false
C19	CG1	VAL- 96	4.46	0	Hydrophobic	false
C26	CG2	VAL- 96	4.23	0	Hydrophobic	false
C11	CG1	VAL- 96	3.93	0	Hydrophobic	false
C17	CG2	VAL- 96	3.62	0	Hydrophobic	false
C7	CB	ALA- 109	4.24	0	Hydrophobic	false
C14	CD	LYS- 111	3.87	0	Hydrophobic	false
C13	CD1	LEU- 159	3.86	0	Hydrophobic	false
O5	N	ALA- 162	3	174.57	H-Bond (Protein Donor)	false
C24	CG	GLU- 166	4.14	0	Hydrophobic	false
N4	O	GLU- 209	3.09	146.09	H-Bond (Ligand Donor)	false
C27	CD2	LEU- 212	4.22	0	Hydrophobic	false
C6	CD1	LEU- 212	3.46	0	Hydrophobic	false
C7	CD1	LEU- 212	3.3	0	Hydrophobic	false
C27	CG2	THR- 222	3.63	0	Hydrophobic	false
C12	CG2	THR- 222	4.07	0	Hydrophobic	false
C13	CG2	THR- 222	3.96	0	Hydrophobic	false
C27	CB	ASP- 223	4.48	0	Hydrophobic	false
C15	CB	ASP- 223	3.97	0	Hydrophobic	false