scPDB - 2wpa entry

Protein Data Bank Entry:

PDB ID : 2wpa

Resolution :2.510 Å

Experimental Method : X-ray

Deposition Date : 2009-08-03

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
C	100 %

Ligand binding site composition:

B-Factor:	55.145
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.562	624.375

% Hydrophobic	% Polar
41.62	58.38
According to VolSite

Ligand :

HET Code:	889
Formula:	C19H32N5O2
Molecular weight:	362.490 g/mol
DrugBank ID:	DB12686
Buried Surface Area:	64.82 %
Polar Surface area:	82.53 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-34.7045	174.563	85.7857

Binding mode :

What is Poseview ?

2D View
3D View

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	CB	ILE- 10	4.07	0	Hydrophobic	false
C15	CZ	TYR- 15	4.07	0	Hydrophobic	false
C15	CG2	VAL- 18	4.49	0	Hydrophobic	false
C23	CG1	VAL- 18	3.95	0	Hydrophobic	false
C23	CB	ALA- 31	3.68	0	Hydrophobic	false
O26	NZ	LYS- 33	3.08	157.93	H-Bond (Protein Donor)	false
C15	CD	LYS- 33	4.35	0	Hydrophobic	false
C22	CG2	VAL- 64	3.89	0	Hydrophobic	false
C22	CG	PHE- 80	3.58	0	Hydrophobic	false
C23	CD1	PHE- 80	3.6	0	Hydrophobic	false
N4	O	GLU- 81	3.14	143.67	H-Bond (Ligand Donor)	false
N5	N	LEU- 83	3.13	177.71	H-Bond (Protein Donor)	false
N7	O	LEU- 83	2.93	137.6	H-Bond (Ligand Donor)	false
C11	CB	GLN- 85	4.38	0	Hydrophobic	false
C11	CD	LYS- 89	4.27	0	Hydrophobic	false
C22	CD1	LEU- 134	4.08	0	Hydrophobic	false
C9	CD2	LEU- 134	4.46	0	Hydrophobic	false
C20	CB	ALA- 144	4.46	0	Hydrophobic	false
C20	CB	ASP- 145	4.02	0	Hydrophobic	false
N17	OD2	ASP- 145	2.64	166.39	H-Bond (Ligand Donor)	false
N17	OD2	ASP- 145	2.64	0	Ionic (Ligand Cationic)	false