scPDB - 1oi9 entry

Protein Data Bank Entry:

PDB ID : 1oi9

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2003-06-10

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:	24.943
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.070	513.000

% Hydrophobic	% Polar
54.61	45.39
According to VolSite

Ligand :

HET Code:	N20
Formula:	C18H21N5O2
Molecular weight:	339.392 g/mol
DrugBank ID:	DB08233
Buried Surface Area:	60.66 %
Polar Surface area:	95.95 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
6.09468	44.2131	51.1302

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
C10	CG2	ILE- 10	3.82	0	Hydrophobic	false
C17	CG2	ILE- 10	3.67	0	Hydrophobic	false
C10	CG1	VAL- 18	4	0	Hydrophobic	false
C11	CG2	VAL- 18	4.38	0	Hydrophobic	false
N9	O	GLU- 81	2.77	155.86	H-Bond (Ligand Donor)	false
N3	N	LEU- 83	3.19	163.91	H-Bond (Protein Donor)	false
N2	O	LEU- 83	2.6	130.93	H-Bond (Ligand Donor)	false
C20	CB	GLN- 85	4.22	0	Hydrophobic	false
O23	OD2	ASP- 86	3.27	150.35	H-Bond (Ligand Donor)	false
C19	CB	ASP- 86	4.31	0	Hydrophobic	false
C18	CD2	LEU- 134	3.96	0	Hydrophobic	false
C15	CB	ASP- 145	4.21	0	Hydrophobic	false