scPDB - 1oir entry

Protein Data Bank Entry:

PDB ID : 1oir

Resolution :1.910 Å

Experimental Method : X-ray

Deposition Date : 2003-06-24

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:	16.756
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.985	664.875

% Hydrophobic	% Polar
48.22	51.78
According to VolSite

Ligand :

HET Code:	HDY
Formula:	C23H27N6O2
Molecular weight:	419.499 g/mol
DrugBank ID:	DB07889
Buried Surface Area:	50.32 %
Polar Surface area:	89.01 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
2.29045	25.5837	7.02548

Binding mode :

What is Poseview ?

2D View
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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
C18	CD1	ILE- 10	4.01	0	Hydrophobic	false
C20	CB	ILE- 10	4.08	0	Hydrophobic	false
C12	CB	ALA- 31	3.44	0	Hydrophobic	false
C10	CE1	PHE- 80	3.8	0	Hydrophobic	false
C12	CB	PHE- 80	4.33	0	Hydrophobic	false
N14	N	LEU- 83	3.08	167.63	H-Bond (Protein Donor)	false
N17	O	LEU- 83	2.84	169.37	H-Bond (Ligand Donor)	false
O31	NZ	LYS- 89	3.05	169.82	H-Bond (Protein Donor)	false
C12	CD1	LEU- 134	3.43	0	Hydrophobic	false
C23	CD2	LEU- 134	4.15	0	Hydrophobic	false
C10	CB	ALA- 144	3.86	0	Hydrophobic	false