scPDB - 2wip entry

Protein Data Bank Entry:

PDB ID : 2wip

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2009-05-14

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:	50.876
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.963	428.625

% Hydrophobic	% Polar
52.76	47.24
According to VolSite

Ligand :

HET Code:	P49
Formula:	C17H14N5O2
Molecular weight:	320.325 g/mol
DrugBank ID:	DB08355
Buried Surface Area:	65.39 %
Polar Surface area:	95.76 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
-35.1205	171.959	86.3987

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
C14	CG1	ILE- 10	4.16	0	Hydrophobic	false
C20	CB	ILE- 10	4.18	0	Hydrophobic	false
C16	CD1	ILE- 10	3.98	0	Hydrophobic	false
C14	CB	VAL- 18	4.45	0	Hydrophobic	false
C5	CB	ALA- 31	3.61	0	Hydrophobic	false
O23	NZ	LYS- 33	3.33	0	Ionic (Protein Cationic)	false
O24	NZ	LYS- 33	2.79	0	Ionic (Protein Cationic)	false
O24	NZ	LYS- 33	2.79	160.67	H-Bond (Protein Donor)	false
C8	CG2	VAL- 64	3.97	0	Hydrophobic	false
C7	CD1	PHE- 80	4.04	0	Hydrophobic	false
C8	CG	PHE- 80	3.53	0	Hydrophobic	false
N2	N	LEU- 83	3.05	165.17	H-Bond (Protein Donor)	false
N15	O	LEU- 83	2.84	171.48	H-Bond (Ligand Donor)	false
C18	CB	ASP- 86	4.37	0	Hydrophobic	false
C19	CD	LYS- 89	4.21	0	Hydrophobic	false
C7	CD1	LEU- 134	4.41	0	Hydrophobic	false
C17	CD2	LEU- 134	3.9	0	Hydrophobic	false
C5	CD1	LEU- 134	3.52	0	Hydrophobic	false
O24	O	HOH- 2026	2.63	147.57	H-Bond (Protein Donor)	false