scPDB - 3tnw entry

Protein Data Bank Entry:

PDB ID : 3tnw

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2011-09-02

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:	32.481
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.672	509.625

% Hydrophobic	% Polar
47.68	52.32
According to VolSite

Ligand :

HET Code:	F18
Formula:	C9H10N6O
Molecular weight:	218.215 g/mol
DrugBank ID:	DB07731
Buried Surface Area:	72.55 %
Polar Surface area:	125.67 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-34.5662	12.8944	30.8972

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
C4	CG2	VAL- 18	4.08	0	Hydrophobic	false
O3	NZ	LYS- 33	2.68	149.47	H-Bond (Protein Donor)	false
C3	CD	LYS- 33	3.72	0	Hydrophobic	false
O3	OE2	GLU- 51	2.62	163.24	H-Bond (Ligand Donor)	false
O3	OE1	GLU- 51	3.43	139.45	H-Bond (Ligand Donor)	false
C2	CG1	VAL- 64	4.28	0	Hydrophobic	false
N18	O	GLU- 81	2.84	155.44	H-Bond (Ligand Donor)	false
N20	O	LEU- 83	2.98	129.83	H-Bond (Ligand Donor)	false
N17	N	LEU- 83	2.8	161.97	H-Bond (Protein Donor)	false
C2	CB	ALA- 144	4.22	0	Hydrophobic	false
C3	CB	ASP- 145	4.08	0	Hydrophobic	false