scPDB - 3rpy entry

Protein Data Bank Entry:

PDB ID : 3rpy

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-04-27

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:	22.371
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.383	526.500

% Hydrophobic	% Polar
44.23	55.77
According to VolSite

Ligand :

HET Code:	27Z
Formula:	C10H11N5O3S2
Molecular weight:	313.356 g/mol
DrugBank ID:	-
Buried Surface Area:	65.2 %
Polar Surface area:	190.8 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:	4

Mass center Coordinates

X	Y	Z
90.7149	81.1921	-48.2082

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
S1	CD1	ILE- 10	3.77	0	Hydrophobic	false
C15	CD1	ILE- 10	3.97	0	Hydrophobic	false
S1	CG2	VAL- 18	4.43	0	Hydrophobic	false
N2	O	GLU- 81	2.79	147.48	H-Bond (Ligand Donor)	false
N1	N	LEU- 83	3.24	172.1	H-Bond (Protein Donor)	false
N3	O	LEU- 83	2.89	124.67	H-Bond (Ligand Donor)	false
O1	N	ASP- 86	3	168.03	H-Bond (Protein Donor)	false
N4	OD2	ASP- 86	3.12	152.62	H-Bond (Ligand Donor)	false
C17	CB	ASP- 86	3.9	0	Hydrophobic	false
O2	NZ	LYS- 89	3.25	175.66	H-Bond (Protein Donor)	false
S1	CD1	LEU- 134	3.94	0	Hydrophobic	false
C16	CD2	LEU- 134	4.08	0	Hydrophobic	false
N22	OD1	ASP- 145	2.94	151.25	H-Bond (Ligand Donor)	false
O2	O	HOH- 318	3.22	159.07	H-Bond (Protein Donor)	false