scPDB - 2b54 entry

Protein Data Bank Entry:

PDB ID : 2b54

Resolution :1.850 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:	27.191
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.446	442.125

% Hydrophobic	% Polar
42.75	57.25
According to VolSite

Ligand :

HET Code:	D05
Formula:	C20H15Cl3N4O3
Molecular weight:	465.717 g/mol
DrugBank ID:	DB07606
Buried Surface Area:	63.68 %
Polar Surface area:	99.74 Å2

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

Mass center Coordinates

X	Y	Z
119.322	-82.9147	93.2888

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
CL12	CG1	ILE- 10	4	0	Hydrophobic	false
C23	CB	ILE- 10	3.6	0	Hydrophobic	false
C24	CG2	ILE- 10	3.68	0	Hydrophobic	false
C1	CG2	VAL- 18	4.11	0	Hydrophobic	false
CL12	CG1	VAL- 18	3.43	0	Hydrophobic	false
C12	CG1	VAL- 18	4	0	Hydrophobic	false
C1	CB	ALA- 31	3.32	0	Hydrophobic	false
N2	NZ	LYS- 33	2.88	165.72	H-Bond (Protein Donor)	false
C2	CG2	VAL- 64	3.69	0	Hydrophobic	false
C2	CB	PHE- 80	3.75	0	Hydrophobic	false
N8	O	LEU- 83	2.73	155.05	H-Bond (Ligand Donor)	false
O9	N	LEU- 83	3.06	166.18	H-Bond (Protein Donor)	false
C20	CB	ASP- 86	4.45	0	Hydrophobic	false
CL14	CB	GLN- 131	4.29	0	Hydrophobic	false
C15	CB	ASN- 132	4.45	0	Hydrophobic	false
CL16	CB	ASN- 132	3.84	0	Hydrophobic	false
C2	CD2	LEU- 134	3.82	0	Hydrophobic	false
CL16	CD1	LEU- 134	4.08	0	Hydrophobic	false
C2	CB	ALA- 144	4.26	0	Hydrophobic	false
CL16	CB	ALA- 144	3.38	0	Hydrophobic	false