scPDB - 2vti entry

Protein Data Bank Entry:

PDB ID : 2vti

Resolution :2.000 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:	22.999
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.954	837.000

% Hydrophobic	% Polar
50.81	49.19
According to VolSite

Ligand :

HET Code:	LZ3
Formula:	C14H12N4O3S
Molecular weight:	316.335 g/mol
DrugBank ID:	DB08133
Buried Surface Area:	64 %
Polar Surface area:	126.32 Å2

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

Mass center Coordinates

X	Y	Z
29.1472	6.93805	63.9834

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
C20	CG2	ILE- 10	3.84	0	Hydrophobic	false
C5	CG2	VAL- 18	4.31	0	Hydrophobic	false
C4	CG1	VAL- 18	3.98	0	Hydrophobic	false
C9	CB	ALA- 31	3.74	0	Hydrophobic	false
C16	CB	ALA- 31	3.44	0	Hydrophobic	false
C7	CG1	VAL- 64	3.53	0	Hydrophobic	false
C7	CB	PHE- 80	3.35	0	Hydrophobic	false
N17	O	GLU- 81	2.8	154.75	H-Bond (Ligand Donor)	false
N1	O	LEU- 83	2.9	136.44	H-Bond (Ligand Donor)	false
N12	N	LEU- 83	3.22	173.29	H-Bond (Protein Donor)	false
O28	N	ASP- 86	3.03	162.93	H-Bond (Protein Donor)	false
C21	CB	ASP- 86	3.78	0	Hydrophobic	false
C20	CD2	LEU- 134	3.78	0	Hydrophobic	false
C9	CD1	LEU- 134	3.33	0	Hydrophobic	false
C16	CD1	LEU- 134	3.36	0	Hydrophobic	false
C6	CB	ALA- 144	4	0	Hydrophobic	false