scPDB - 2vtj entry

Protein Data Bank Entry:

PDB ID : 2vtj

Resolution :2.200 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:	33.614
Number of residues:	22
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.625	627.750

% Hydrophobic	% Polar
43.01	56.99
According to VolSite

Ligand :

HET Code:	LZ4
Formula:	C10H9ClN4O2S
Molecular weight:	284.722 g/mol
DrugBank ID:	DB08134
Buried Surface Area:	60.64 %
Polar Surface area:	106.35 Å2

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

Mass center Coordinates

X	Y	Z
29.9515	7.47117	64.3523

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
C8	CD1	ILE- 10	3.84	0	Hydrophobic	false
C7	CB	ILE- 10	3.97	0	Hydrophobic	false
CL1	CB	ALA- 31	3.89	0	Hydrophobic	false
CL1	CG1	VAL- 64	4.12	0	Hydrophobic	false
CL1	CB	PHE- 80	3.75	0	Hydrophobic	false
N12	N	LEU- 83	2.86	169.68	H-Bond (Protein Donor)	false
O4	N	ASP- 86	2.89	158.11	H-Bond (Protein Donor)	false
C18	CB	ASP- 86	4.43	0	Hydrophobic	false
CL1	CD1	LEU- 134	4.17	0	Hydrophobic	false
C17	CD2	LEU- 134	4.12	0	Hydrophobic	false
CL1	CB	ALA- 144	4.15	0	Hydrophobic	false
N1	O	HOH- 2033	3.37	166.8	H-Bond (Ligand Donor)	false