scPDB - 3s2p entry

Protein Data Bank Entry:

PDB ID : 3s2p

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2011-05-17

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:	42.090
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.781	715.500

% Hydrophobic	% Polar
50.47	49.53
According to VolSite

Ligand :

HET Code:	PMU
Formula:	C17H22N4O3
Molecular weight:	330.382 g/mol
DrugBank ID:	-
Buried Surface Area:	54.63 %
Polar Surface area:	115.73 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
24.3938	27.4766	27.4376

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
C7	CG2	ILE- 10	4.42	0	Hydrophobic	false
C20	CG2	ILE- 10	4	0	Hydrophobic	false
C1	CG2	VAL- 18	3.63	0	Hydrophobic	false
C3	CB	ALA- 31	3.52	0	Hydrophobic	false
O3	NZ	LYS- 33	2.66	138.27	H-Bond (Protein Donor)	false
C18	CG	GLN- 85	3.73	0	Hydrophobic	false
C12	CB	ASP- 86	3.85	0	Hydrophobic	false
C18	CB	LYS- 89	3.69	0	Hydrophobic	false
C10	CB	ASN- 132	3.88	0	Hydrophobic	false
C8	CD2	LEU- 134	4.19	0	Hydrophobic	false
C20	CD2	LEU- 134	4.25	0	Hydrophobic	false
C3	CD1	LEU- 134	3.55	0	Hydrophobic	false
C6	CD2	LEU- 134	3.52	0	Hydrophobic	false
C8	CB	ALA- 144	3.81	0	Hydrophobic	false
O3	OD1	ASP- 145	3.12	142.57	H-Bond (Ligand Donor)	false