scPDB - 1oit entry

Protein Data Bank Entry:

PDB ID : 1oit

Resolution :1.600 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:	20.006
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.884	705.375

% Hydrophobic	% Polar
48.33	51.67
According to VolSite

Ligand :

HET Code:	HDT
Formula:	C17H15N6O2S
Molecular weight:	367.405 g/mol
DrugBank ID:	DB02197
Buried Surface Area:	62.79 %
Polar Surface area:	124.89 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
11.5317	-9.36058	10.502

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
C22	CG1	ILE- 10	4.27	0	Hydrophobic	false
C18	CG2	ILE- 10	4.09	0	Hydrophobic	false
C11	CB	ALA- 31	3.38	0	Hydrophobic	false
N7	NZ	LYS- 33	3.38	131.65	H-Bond (Protein Donor)	false
C11	CB	PHE- 80	4.48	0	Hydrophobic	false
N16	O	LEU- 83	2.72	146.39	H-Bond (Ligand Donor)	false
N13	N	LEU- 83	3.29	173.28	H-Bond (Protein Donor)	false
O26	N	ASP- 86	3.08	167.58	H-Bond (Protein Donor)	false
N24	OD2	ASP- 86	2.83	158.08	H-Bond (Ligand Donor)	false
C19	CB	ASP- 86	3.88	0	Hydrophobic	false
C11	CD1	LEU- 134	3.56	0	Hydrophobic	false
C18	CD2	LEU- 134	3.79	0	Hydrophobic	false