scPDB - 3r1y entry

Protein Data Bank Entry:

PDB ID : 3r1y

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2011-03-11

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:	26.558
Number of residues:	24
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.738	776.250

% Hydrophobic	% Polar
43.04	56.96
According to VolSite

Ligand :

HET Code:	X76
Formula:	C13H13N3O
Molecular weight:	227.262 g/mol
DrugBank ID:	-
Buried Surface Area:	54.26 %
Polar Surface area:	68 Å2

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

Mass center Coordinates

X	Y	Z
119.354	-25.7616	-47.8992

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
C12	CG2	ILE- 10	3.68	0	Hydrophobic	false
C16	CG2	ILE- 10	3.8	0	Hydrophobic	false
C07	CG2	ILE- 10	3.36	0	Hydrophobic	false
C09	CG1	VAL- 18	3.81	0	Hydrophobic	false
C04	CB	ALA- 31	4.15	0	Hydrophobic	false
N02	O	GLU- 81	3.13	170.77	H-Bond (Ligand Donor)	false
N01	O	LEU- 83	2.92	128.62	H-Bond (Ligand Donor)	false
O17	N	LEU- 83	2.97	174.55	H-Bond (Protein Donor)	false
C07	CD2	LEU- 134	4.12	0	Hydrophobic	false
C11	CD2	LEU- 134	3.81	0	Hydrophobic	false
C05	CD1	LEU- 134	3.62	0	Hydrophobic	false