scPDB - 3dog entry

Protein Data Bank Entry:

PDB ID : 3dog

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2008-07-04

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
C	100 %

Ligand binding site composition:

B-Factor:	5.912
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.729	469.125

% Hydrophobic	% Polar
48.92	51.08
According to VolSite

Ligand :

HET Code:	NNN
Formula:	C19H26N6O
Molecular weight:	354.449 g/mol
DrugBank ID:	DB08285
Buried Surface Area:	68.01 %
Polar Surface area:	87.37 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-33.4172	-18.0841	-30.6848

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'	CG1	ILE- 10	3.92	0	Hydrophobic	false
C2'	CG2	ILE- 10	3.58	0	Hydrophobic	false
C15	CG2	VAL- 18	4.28	0	Hydrophobic	false
C10	CG1	VAL- 18	3.63	0	Hydrophobic	false
C9	CB	ALA- 31	3.92	0	Hydrophobic	false
C11	CG2	VAL- 64	3.72	0	Hydrophobic	false
C9	CB	PHE- 80	3.67	0	Hydrophobic	false
C10	CD1	PHE- 80	3.65	0	Hydrophobic	false
C11	CG	PHE- 80	3.97	0	Hydrophobic	false
N7	N	LEU- 83	3.27	168.87	H-Bond (Protein Donor)	false
N6	O	LEU- 83	2.82	138.42	H-Bond (Ligand Donor)	false
CA'	CD2	LEU- 134	4.17	0	Hydrophobic	false
C11	CD1	LEU- 134	3.95	0	Hydrophobic	false
C14	CB	ALA- 144	3.75	0	Hydrophobic	false
C11	CB	ALA- 144	4.06	0	Hydrophobic	false
C14	CB	ASP- 145	3.78	0	Hydrophobic	false
N2	O	HOH- 337	3.08	133.25	H-Bond (Ligand Donor)	false