scPDB - 4ekl entry

Protein Data Bank Entry:

PDB ID : 4ekl

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-04-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	RAC-alpha serine/threonine-protein kinase
ID:	AKT1_HUMAN
AC:	P31749
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:	32.721
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.562	965.250

% Hydrophobic	% Polar
41.61	58.39
According to VolSite

Ligand :

HET Code:	0RF
Formula:	C24H33ClN5O2
Molecular weight:	459.004 g/mol
DrugBank ID:	DB11743
Buried Surface Area:	60.13 %
Polar Surface area:	86.17 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
28.0319	5.22134	10.8912

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- 156	3.75	0	Hydrophobic	false
C5	CG1	VAL- 164	4.42	0	Hydrophobic	false
C11	CG2	VAL- 164	3.94	0	Hydrophobic	false
C13	CB	VAL- 164	4.06	0	Hydrophobic	false
C17	CG2	VAL- 164	3.83	0	Hydrophobic	false
CL1	CG2	VAL- 164	4.08	0	Hydrophobic	false
C27	CG2	VAL- 164	3.63	0	Hydrophobic	false
C5	CB	ALA- 177	4.21	0	Hydrophobic	false
C7	CB	ALA- 177	4.11	0	Hydrophobic	false
CL1	CG	LYS- 179	3.8	0	Hydrophobic	false
CL1	CD2	LEU- 181	4.17	0	Hydrophobic	false
C8	CG2	THR- 211	3.82	0	Hydrophobic	false
C8	CE	MET- 227	4.46	0	Hydrophobic	false
C11	CE	MET- 227	3.6	0	Hydrophobic	false
O12	O	GLU- 228	2.66	146.34	H-Bond (Ligand Donor)	false
N3	N	ALA- 230	2.97	171.66	H-Bond (Protein Donor)	false
C7	CB	ALA- 230	4.45	0	Hydrophobic	false
N23	OE2	GLU- 234	2.96	133.62	H-Bond (Ligand Donor)	false
N23	OE2	GLU- 234	2.96	0	Ionic (Ligand Cationic)	false
N23	OE2	GLU- 278	2.75	143.93	H-Bond (Ligand Donor)	false
N23	OE2	GLU- 278	2.75	0	Ionic (Ligand Cationic)	false
C30	CG	GLU- 278	3.93	0	Hydrophobic	false
C17	SD	MET- 281	4.34	0	Hydrophobic	false
C5	SD	MET- 281	3.55	0	Hydrophobic	false
C8	CB	THR- 291	3.97	0	Hydrophobic	false
C13	CE2	PHE- 438	3.98	0	Hydrophobic	false