scPDB - 4fkw entry

Protein Data Bank Entry:

PDB ID : 4fkw

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2012-06-13

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:	29.840
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.914	502.875

% Hydrophobic	% Polar
50.34	49.66
According to VolSite

Ligand :

HET Code:	62K
Formula:	C19H20N4O5S
Molecular weight:	416.451 g/mol
DrugBank ID:	-
Buried Surface Area:	66.46 %
Polar Surface area:	148.32 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-12.28	-8.82597	-10.8158

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
CAU	CD1	ILE- 10	4.1	0	Hydrophobic	false
CAV	CG2	VAL- 18	4.14	0	Hydrophobic	false
CAN	CG1	VAL- 18	3.98	0	Hydrophobic	false
CAO	CG2	VAL- 18	3.77	0	Hydrophobic	false
CAM	CB	ALA- 31	4.12	0	Hydrophobic	false
CBA	CB	ALA- 31	4.12	0	Hydrophobic	false
OAD	NZ	LYS- 33	2.9	170.94	H-Bond (Protein Donor)	false
CAM	CG2	VAL- 64	4.07	0	Hydrophobic	false
CAM	CB	PHE- 80	3.61	0	Hydrophobic	false
N5	O	GLU- 81	2.98	161.75	H-Bond (Ligand Donor)	false
OAE	N	LEU- 83	2.88	170.75	H-Bond (Protein Donor)	false
OAG	N	ASP- 86	3.05	156.55	H-Bond (Protein Donor)	false
CAK	CB	ASP- 86	3.79	0	Hydrophobic	false
CAA	CB	ASN- 132	4.4	0	Hydrophobic	false
CAI	CD2	LEU- 134	4	0	Hydrophobic	false
CBA	CD1	LEU- 134	3.69	0	Hydrophobic	false
CAL	CB	ALA- 144	4.12	0	Hydrophobic	false
CAO	CB	ASP- 145	3.81	0	Hydrophobic	false