scPDB - 1w8c entry

Protein Data Bank Entry:

PDB ID : 1w8c

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2004-09-20

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:	18.814
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.631	853.875

% Hydrophobic	% Polar
38.74	61.26
According to VolSite

Ligand :

HET Code:	N69
Formula:	C15H23N5O
Molecular weight:	289.376 g/mol
DrugBank ID:	DB08247
Buried Surface Area:	54.97 %
Polar Surface area:	89.71 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
39.0402	-9.23419	10.4941

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
C17	CG2	ILE- 10	3.83	0	Hydrophobic	false
C19	CD1	ILE- 10	4.36	0	Hydrophobic	false
C10	CG2	ILE- 10	4.2	0	Hydrophobic	false
C10	CG1	VAL- 18	3.75	0	Hydrophobic	false
C12	CG2	VAL- 18	4.1	0	Hydrophobic	false
N1	NZ	LYS- 33	3.19	147.48	H-Bond (Protein Donor)	false
N2	O	GLU- 81	2.63	155.99	H-Bond (Ligand Donor)	false
C19	CZ	PHE- 82	3.63	0	Hydrophobic	false
N3	N	LEU- 83	3.45	174.4	H-Bond (Protein Donor)	false
N9	O	LEU- 83	2.59	147.68	H-Bond (Ligand Donor)	false
C18	CB	ASP- 86	4.47	0	Hydrophobic	false
C15	CB	ASN- 132	3.76	0	Hydrophobic	false