scPDB - 1di8 entry

Protein Data Bank Entry:

PDB ID : 1di8

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1999-11-29

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:	36.536
Number of residues:	31
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.286	600.750

% Hydrophobic	% Polar
54.49	45.51
According to VolSite

Ligand :

HET Code:	DTQ
Formula:	C16H15N3O3
Molecular weight:	297.309 g/mol
DrugBank ID:	DB03365
Buried Surface Area:	62.04 %
Polar Surface area:	76.5 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-8.77327	50.0573	12.795

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
C32	CG2	ILE- 10	3.44	0	Hydrophobic	false
C10	CG2	ILE- 10	3.5	0	Hydrophobic	false
C9	CG2	ILE- 10	3.29	0	Hydrophobic	false
C14	CG1	VAL- 18	4.34	0	Hydrophobic	false
C15	CG2	VAL- 18	3.85	0	Hydrophobic	false
C17	CD	LYS- 33	3.72	0	Hydrophobic	false
C19	CB	PHE- 80	4.38	0	Hydrophobic	false
C27	CZ	PHE- 82	3.91	0	Hydrophobic	false
N3	N	LEU- 83	2.8	168.41	H-Bond (Protein Donor)	false
C32	CB	ASP- 86	4.17	0	Hydrophobic	false
C10	CD2	LEU- 134	3.61	0	Hydrophobic	false
C19	CB	ALA- 144	3.86	0	Hydrophobic	false
C17	CB	ASP- 145	4.32	0	Hydrophobic	false
O21	OD1	ASP- 145	2.7	134.98	H-Bond (Ligand Donor)	false
O26	O	HOH- 600	3.17	179.95	H-Bond (Protein Donor)	false
O21	O	HOH- 604	3.29	129.28	H-Bond (Ligand Donor)	false