scPDB - 4lyn entry

Protein Data Bank Entry:

PDB ID : 4lyn

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2013-07-31

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:	31.824
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.627	536.625

% Hydrophobic	% Polar
50.94	49.06
According to VolSite

Ligand :

HET Code:	1YG
Formula:	C20H23N3O2S2
Molecular weight:	401.546 g/mol
DrugBank ID:	-
Buried Surface Area:	63.24 %
Polar Surface area:	121.56 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
25.7168	28.4048	27.8056

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
C12	CG2	ILE- 10	4.17	0	Hydrophobic	false
S13	CG2	ILE- 10	3.9	0	Hydrophobic	false
C24	CG2	ILE- 10	3.9	0	Hydrophobic	false
C25	CG1	ILE- 10	4.14	0	Hydrophobic	false
C10	CG2	VAL- 18	3.88	0	Hydrophobic	false
S6	CG1	VAL- 18	4.32	0	Hydrophobic	false
S13	CG1	VAL- 18	4.11	0	Hydrophobic	false
S6	CB	ALA- 31	3.51	0	Hydrophobic	false
S13	CB	ALA- 31	4.08	0	Hydrophobic	false
C3	CG1	VAL- 64	4.47	0	Hydrophobic	false
C3	CG	PHE- 80	4.39	0	Hydrophobic	false
S6	CB	PHE- 80	3.61	0	Hydrophobic	false
N16	N	LEU- 83	3.09	166.69	H-Bond (Protein Donor)	false
N17	O	LEU- 83	2.75	166.45	H-Bond (Ligand Donor)	false
C22	CB	ASP- 86	3.86	0	Hydrophobic	false
C3	CD1	LEU- 134	4.32	0	Hydrophobic	false
C22	CD2	LEU- 134	4.27	0	Hydrophobic	false
S13	CD1	LEU- 134	4.04	0	Hydrophobic	false
C3	CB	ALA- 144	3.68	0	Hydrophobic	false