scPDB - 2b53 entry

Protein Data Bank Entry:

PDB ID : 2b53

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2005-09-27

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:	30.425
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.776	651.375

% Hydrophobic	% Polar
39.38	60.62
According to VolSite

Ligand :

HET Code:	D23
Formula:	C19H19F3N4
Molecular weight:	360.376 g/mol
DrugBank ID:	DB07612
Buried Surface Area:	57.65 %
Polar Surface area:	63.83 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
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
80.2256	64.7307	55.6413

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
C5	CB	ILE- 10	4.41	0	Hydrophobic	false
C10	CD1	ILE- 10	3.74	0	Hydrophobic	false
C21	CG2	VAL- 18	3.92	0	Hydrophobic	false
F26	CG1	VAL- 18	3.96	0	Hydrophobic	false
F25	CB	ALA- 31	3.62	0	Hydrophobic	false
F26	CB	LYS- 33	4.32	0	Hydrophobic	false
F25	CG2	VAL- 64	4.27	0	Hydrophobic	false
F25	CB	PHE- 80	3.27	0	Hydrophobic	false
F26	CD2	PHE- 80	3.22	0	Hydrophobic	false
C2	CG	GLN- 85	4.36	0	Hydrophobic	false
C1	CB	ASP- 86	4.1	0	Hydrophobic	false
N7	OD2	ASP- 86	3.18	167.09	H-Bond (Ligand Donor)	false
N7	OD1	ASP- 86	3.24	126.35	H-Bond (Ligand Donor)	false
C2	CG	LYS- 89	4.17	0	Hydrophobic	false
C20	CB	ASN- 132	3.72	0	Hydrophobic	false
C10	CD2	LEU- 134	4.41	0	Hydrophobic	false
F25	CD2	LEU- 134	4.5	0	Hydrophobic	false
C12	CD1	LEU- 134	4.34	0	Hydrophobic	false
C20	CB	ALA- 144	4.26	0	Hydrophobic	false
F24	CB	ALA- 144	3.87	0	Hydrophobic	false
N14	O	HOH- 308	3	179.98	H-Bond (Protein Donor)	false
N18	O	HOH- 339	3.35	134.06	H-Bond (Ligand Donor)	false