scPDB - 2vtp entry

Protein Data Bank Entry:

PDB ID : 2vtp

Resolution :2.150 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:	37.953
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.907	695.250

% Hydrophobic	% Polar
47.57	52.43
According to VolSite

Ligand :

HET Code:	LZ9
Formula:	C17H11F3N4O2
Molecular weight:	360.290 g/mol
DrugBank ID:	DB08138
Buried Surface Area:	64.74 %
Polar Surface area:	86.88 Å2

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

Mass center Coordinates

X	Y	Z
27.699	6.78558	63.44

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
C4	CG2	ILE- 10	3.86	0	Hydrophobic	false
F19	CG2	VAL- 18	3.5	0	Hydrophobic	false
C20	CG2	VAL- 18	3.56	0	Hydrophobic	false
F19	CD	LYS- 33	3.29	0	Hydrophobic	false
F19	CD2	PHE- 80	4.41	0	Hydrophobic	false
N6	O	LEU- 83	2.52	133.65	H-Bond (Ligand Donor)	false
N10	N	LEU- 83	2.99	165.44	H-Bond (Protein Donor)	false
C26	CB	ASP- 86	4.34	0	Hydrophobic	false
F24	CB	ASN- 132	4.08	0	Hydrophobic	false
F24	CD2	LEU- 134	3.89	0	Hydrophobic	false
C25	CD2	LEU- 134	3.79	0	Hydrophobic	false
F24	CB	ALA- 144	3.48	0	Hydrophobic	false
O16	O	HOH- 2204	2.55	156.79	H-Bond (Protein Donor)	false