scPDB - 2c6k entry

Protein Data Bank Entry:

PDB ID : 2c6k

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2005-11-10

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:	27.470
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.620	607.500

% Hydrophobic	% Polar
38.33	61.67
According to VolSite

Ligand :

HET Code:	DT2
Formula:	C17H21N7O2S
Molecular weight:	387.459 g/mol
DrugBank ID:	DB07686
Buried Surface Area:	64.93 %
Polar Surface area:	135.67 Å2

Number of
H-Bond Acceptors:	7
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
11.082	-9.75374	9.69041

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
C13	CD1	ILE- 10	4.4	0	Hydrophobic	false
C2	CG1	ILE- 10	4.37	0	Hydrophobic	false
C14	CG2	ILE- 10	3.88	0	Hydrophobic	false
C2	CB	VAL- 18	4.18	0	Hydrophobic	false
N1	NZ	LYS- 33	2.79	139.43	H-Bond (Protein Donor)	false
N5	O	LEU- 83	2.74	125.97	H-Bond (Ligand Donor)	false
N3	N	LEU- 83	3.23	169.9	H-Bond (Protein Donor)	false
O3	N	ASP- 86	3.23	159.36	H-Bond (Protein Donor)	false
C17	CB	ASP- 86	3.85	0	Hydrophobic	false
C5	CB	GLN- 131	4.23	0	Hydrophobic	false
C18	CD2	LEU- 134	3.65	0	Hydrophobic	false