scPDB - 4cfn entry

Protein Data Bank Entry:

PDB ID : 4cfn

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2013-11-19

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:	34.620
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.061	462.375

% Hydrophobic	% Polar
60.58	39.42
According to VolSite

Ligand :

HET Code:	JYM
Formula:	C13H16F3N5O
Molecular weight:	315.294 g/mol
DrugBank ID:	-
Buried Surface Area:	52.7 %
Polar Surface area:	89.71 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
4.91823	44.8729	51.299

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
CAN	CG2	ILE- 10	4.23	0	Hydrophobic	false
FAV	CG1	VAL- 18	3.8	0	Hydrophobic	false
C5	CG1	VAL- 18	4.25	0	Hydrophobic	false
FAT	CB	ALA- 31	4.07	0	Hydrophobic	false
FAV	CD	LYS- 33	4.17	0	Hydrophobic	false
FAT	CG2	VAL- 64	3.77	0	Hydrophobic	false
FAT	CB	PHE- 80	3.22	0	Hydrophobic	false
FAV	CD2	PHE- 80	3.26	0	Hydrophobic	false
N3	O	LEU- 83	2.85	129.31	H-Bond (Ligand Donor)	false
N2	O	LEU- 83	2.74	135.88	H-Bond (Ligand Donor)	false
CAL	CB	ASP- 86	4.3	0	Hydrophobic	false
FAU	CD1	LEU- 134	4.45	0	Hydrophobic	false
C5	CD1	LEU- 134	3.61	0	Hydrophobic	false
CAL	CD2	LEU- 134	3.95	0	Hydrophobic	false
FAU	CB	ALA- 144	4.45	0	Hydrophobic	false