scPDB - 2vts entry

Protein Data Bank Entry:

PDB ID : 2vts

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2008-05-15

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:	33.120
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.392	725.625

% Hydrophobic	% Polar
37.67	62.33
According to VolSite

Ligand :

HET Code:	LZC
Formula:	C16H24N7
Molecular weight:	314.409 g/mol
DrugBank ID:	DB08140
Buried Surface Area:	65.91 %
Polar Surface area:	105.68 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
27.359	7.37396	63.3283

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
C2	CD1	ILE- 10	4.39	0	Hydrophobic	false
C10	CG2	VAL- 18	3.89	0	Hydrophobic	false
N20	NZ	LYS- 33	2.82	148.31	H-Bond (Protein Donor)	false
C1	CZ	PHE- 82	3.51	0	Hydrophobic	false
C2	CE1	PHE- 82	4.48	0	Hydrophobic	false
N4	O	LEU- 83	2.83	130.66	H-Bond (Ligand Donor)	false
N22	N	LEU- 83	3.3	167.7	H-Bond (Protein Donor)	false
N13	OD1	ASN- 132	2.87	146.7	H-Bond (Ligand Donor)	false
C3	CD2	LEU- 134	4.23	0	Hydrophobic	false
N13	OD2	ASP- 145	2.93	0	Ionic (Ligand Cationic)	false