scPDB - 1ke7 entry

Protein Data Bank Entry:

PDB ID : 1ke7

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2001-11-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclin-dependent kinase 2
ID:	CDK2_HUMAN
AC:	P24941
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.22

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	39.006
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.769	553.500

% Hydrophobic	% Polar
43.29	56.71
According to VolSite

Ligand :

HET Code:	LS3
Formula:	C20H15N3O4S
Molecular weight:	393.416 g/mol
DrugBank ID:	DB08124
Buried Surface Area:	61.41 %
Polar Surface area:	109.68 Å2

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

Mass center Coordinates

X	Y	Z
-9.10954	48.3149	11.804

Binding mode :

What is Poseview ?

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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
C32	CD1	ILE- 10	3.7	0	Hydrophobic	false
C22	CG2	ILE- 10	3.49	0	Hydrophobic	false
C11	CG2	VAL- 18	4.14	0	Hydrophobic	false
C17	CG1	VAL- 18	4.26	0	Hydrophobic	false
C9	CB	ALA- 31	4.43	0	Hydrophobic	false
C18	CB	ALA- 31	4.26	0	Hydrophobic	false
O13	NZ	LYS- 33	3.04	160.2	H-Bond (Protein Donor)	false
DuAr	NZ	LYS- 33	3.93	104.32	Pi/Cation	false
C9	CG1	VAL- 64	4.26	0	Hydrophobic	false
C9	CB	PHE- 80	3.7	0	Hydrophobic	false
N7	O	GLU- 81	3	138.2	H-Bond (Ligand Donor)	false
O5	N	LEU- 83	2.68	153.27	H-Bond (Protein Donor)	false
N21	O	LEU- 83	2.84	137.79	H-Bond (Ligand Donor)	false
C25	CB	ASP- 86	4.06	0	Hydrophobic	false
O28	N	ASP- 86	3.33	162.8	H-Bond (Protein Donor)	false
C29	CD	LYS- 89	4.34	0	Hydrophobic	false
C23	CD2	LEU- 134	4.09	0	Hydrophobic	false
C18	CD1	LEU- 134	3.62	0	Hydrophobic	false
C11	CB	ALA- 144	4.27	0	Hydrophobic	false
C10	CB	ALA- 144	4.04	0	Hydrophobic	false