scPDB - 3rk5 entry

Protein Data Bank Entry:

PDB ID : 3rk5

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2011-04-17

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:	30.533
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.983	540.000

% Hydrophobic	% Polar
49.38	50.63
According to VolSite

Ligand :

HET Code:	07Z
Formula:	C16H11N4O3S
Molecular weight:	339.349 g/mol
DrugBank ID:	-
Buried Surface Area:	61.53 %
Polar Surface area:	149.27 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
91.7288	116.786	-47.9556

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
S7	CD1	ILE- 10	4.15	0	Hydrophobic	false
C1	CD1	ILE- 10	4.02	0	Hydrophobic	false
C10	CG1	VAL- 18	4.26	0	Hydrophobic	false
N8	O	GLU- 81	2.74	147.55	H-Bond (Ligand Donor)	false
N2	O	LEU- 83	2.57	147.79	H-Bond (Ligand Donor)	false
N4	N	LEU- 83	3.25	175.31	H-Bond (Protein Donor)	false
C20	CB	ASP- 86	4.18	0	Hydrophobic	false
S7	CD2	LEU- 134	3.8	0	Hydrophobic	false
C11	CD2	LEU- 134	4.16	0	Hydrophobic	false
C21	CD2	LEU- 134	4.39	0	Hydrophobic	false
C11	CB	ALA- 144	4.2	0	Hydrophobic	false