scPDB - 1y8y entry

Protein Data Bank Entry:

PDB ID : 1y8y

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2004-12-14

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:	37.358
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.459	604.125

% Hydrophobic	% Polar
37.43	62.57
According to VolSite

Ligand :

HET Code:	CT7
Formula:	C13H11ClN4O2S
Molecular weight:	322.770 g/mol
DrugBank ID:	DB02963
Buried Surface Area:	59.25 %
Polar Surface area:	84.74 Å2

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

Mass center Coordinates

X	Y	Z
23.3958	27.9727	28.3721

Binding mode :

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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
C14	CB	ILE- 10	4.39	0	Hydrophobic	false
CL1	CG2	VAL- 18	3.78	0	Hydrophobic	false
N1	NZ	LYS- 33	3.09	151.78	H-Bond (Protein Donor)	false
N5	O	LEU- 83	2.84	131.31	H-Bond (Ligand Donor)	false
N3	N	LEU- 83	3.22	174.25	H-Bond (Protein Donor)	false
O2	N	ASP- 86	3.1	159.12	H-Bond (Protein Donor)	false
C17	CB	ASP- 86	3.84	0	Hydrophobic	false
O3	NZ	LYS- 89	3.44	121.39	H-Bond (Protein Donor)	false
C20	CD	LYS- 89	4.16	0	Hydrophobic	false
C18	CD2	LEU- 134	3.43	0	Hydrophobic	false