scPDB - 2r64 entry

Protein Data Bank Entry:

PDB ID : 2r64

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2007-09-05

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:	40.612
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.869	651.375

% Hydrophobic	% Polar
50.78	49.22
According to VolSite

Ligand :

HET Code:	740
Formula:	C23H27N5O3S
Molecular weight:	453.557 g/mol
DrugBank ID:	DB07220
Buried Surface Area:	55.47 %
Polar Surface area:	106.78 Å2

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

Mass center Coordinates

X	Y	Z
24.7922	27.3202	28.9244

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
C23	CG	GLU- 8	3.96	0	Hydrophobic	false
C11	CD1	ILE- 10	3.84	0	Hydrophobic	false
C3	CG2	ILE- 10	3.54	0	Hydrophobic	false
C6	CD1	ILE- 10	3.61	0	Hydrophobic	false
C16	CG1	VAL- 18	4.11	0	Hydrophobic	false
C22	CG2	VAL- 18	3.42	0	Hydrophobic	false
C13	CB	ALA- 31	3.39	0	Hydrophobic	false
C14	CG1	VAL- 64	4.36	0	Hydrophobic	false
C14	CB	PHE- 80	3.6	0	Hydrophobic	false
N12	O	GLU- 81	2.6	159.53	H-Bond (Ligand Donor)	false
N9	O	LEU- 83	2.6	174.2	H-Bond (Ligand Donor)	false
N11	N	LEU- 83	2.82	156.43	H-Bond (Protein Donor)	false
C18	CD1	LEU- 134	3.5	0	Hydrophobic	false