scPDB - 3r83 entry

Protein Data Bank Entry:

PDB ID : 3r83

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2011-03-23

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:	16.861
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.107	911.250

% Hydrophobic	% Polar
41.48	58.52
According to VolSite

Ligand :

HET Code:	Z14
Formula:	C17H23N8O3
Molecular weight:	387.416 g/mol
DrugBank ID:	-
Buried Surface Area:	58.48 %
Polar Surface area:	183.61 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-79.7978	100.765	8.07129

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	4.03	0	Hydrophobic	false
C21	CG2	ILE- 10	3.91	0	Hydrophobic	false
C12	CG2	ILE- 10	3.55	0	Hydrophobic	false
N06	O	GLU- 12	3.25	133.2	H-Bond (Ligand Donor)	false
C09	CG1	VAL- 18	4.31	0	Hydrophobic	false
C21	CG2	VAL- 18	4.19	0	Hydrophobic	false
C09	CB	ALA- 31	4.31	0	Hydrophobic	false
O27	NZ	LYS- 33	3.74	0	Ionic (Protein Cationic)	false
O28	NZ	LYS- 33	3.21	0	Ionic (Protein Cationic)	false
O28	NZ	LYS- 33	3.21	123.89	H-Bond (Protein Donor)	false
N02	O	GLU- 81	3.07	174.21	H-Bond (Ligand Donor)	false
N01	O	LEU- 83	3.02	127.61	H-Bond (Ligand Donor)	false
O26	N	LEU- 83	3.08	172.27	H-Bond (Protein Donor)	false
C23	CB	ASP- 86	4.44	0	Hydrophobic	false
C24	CB	GLN- 131	4.12	0	Hydrophobic	false
C12	CD2	LEU- 134	4.11	0	Hydrophobic	false
C16	CD2	LEU- 134	4.09	0	Hydrophobic	false
C10	CD1	LEU- 134	3.61	0	Hydrophobic	false