scPDB - 3ezv entry

Protein Data Bank Entry:

PDB ID : 3ezv

Resolution :1.990 Å

Experimental Method : X-ray

Deposition Date : 2008-10-23

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:	46.228
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.623	928.125

% Hydrophobic	% Polar
38.55	61.45
According to VolSite

Ligand :

HET Code:	EZV
Formula:	C25H26N7
Molecular weight:	424.521 g/mol
DrugBank ID:	-
Buried Surface Area:	54 %
Polar Surface area:	91.06 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	6
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
0.732781	29.1367	9.16641

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
C12	CD1	ILE- 10	4.07	0	Hydrophobic	false
C18	CG2	ILE- 10	3.76	0	Hydrophobic	false
C21	CG2	ILE- 10	4.26	0	Hydrophobic	false
C6	CG1	VAL- 18	4.38	0	Hydrophobic	false
C4	CB	ALA- 31	3.46	0	Hydrophobic	false
C28	CD	LYS- 33	3.85	0	Hydrophobic	false
C31	CG1	VAL- 64	4.26	0	Hydrophobic	false
C3	CG1	VAL- 64	3.85	0	Hydrophobic	false
C31	CB	PHE- 80	4.37	0	Hydrophobic	false
C3	CB	PHE- 80	3.62	0	Hydrophobic	false
DuAr	DuAr	PHE- 80	3.47	0	Aromatic Face/Face	false
N7	O	GLU- 81	2.76	168.03	H-Bond (Ligand Donor)	false
N8	N	LEU- 83	3.16	168.65	H-Bond (Protein Donor)	false
N11	O	LEU- 83	2.53	136.36	H-Bond (Ligand Donor)	false
C21	CB	ASP- 86	4.09	0	Hydrophobic	false
N23	OD2	ASP- 86	3.55	0	Ionic (Ligand Cationic)	false
C21	CD2	LEU- 134	4.29	0	Hydrophobic	false
C5	CD1	LEU- 134	3.3	0	Hydrophobic	false
C2	CB	ALA- 144	4.1	0	Hydrophobic	false
C31	CB	ALA- 144	3.66	0	Hydrophobic	false
C28	CB	ASP- 145	4.12	0	Hydrophobic	false