scPDB - 3lfn entry

Protein Data Bank Entry:

PDB ID : 3lfn

Resolution :2.280 Å

Experimental Method : X-ray

Deposition Date : 2010-01-18

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:	41.144
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.059	978.750

% Hydrophobic	% Polar
42.76	57.24
According to VolSite

Ligand :

HET Code:	A27
Formula:	C23H21N3O2
Molecular weight:	371.432 g/mol
DrugBank ID:	-
Buried Surface Area:	65.57 %
Polar Surface area:	78.01 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
39.7672	-8.63114	24.0642

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
C2	CG2	ILE- 10	4.03	0	Hydrophobic	false
C37	CG1	ILE- 10	4.34	0	Hydrophobic	false
C17	CG2	ILE- 10	3.77	0	Hydrophobic	false
C25	CG2	VAL- 18	4.03	0	Hydrophobic	false
C2	CG2	VAL- 18	3.57	0	Hydrophobic	false
C12	CG1	VAL- 18	4.21	0	Hydrophobic	false
C15	CB	ALA- 31	3.54	0	Hydrophobic	false
C24	CD	LYS- 33	3.48	0	Hydrophobic	false
C14	CG1	VAL- 64	4.07	0	Hydrophobic	false
C21	CG1	VAL- 64	4.16	0	Hydrophobic	false
C14	CB	PHE- 80	4.16	0	Hydrophobic	false
C21	CB	PHE- 80	4.39	0	Hydrophobic	false
DuAr	DuAr	PHE- 80	3.98	0	Aromatic Face/Face	false
N31	O	GLU- 81	2.9	170.33	H-Bond (Ligand Donor)	false
C37	CE1	PHE- 82	3.7	0	Hydrophobic	false
C40	CZ	PHE- 82	4.32	0	Hydrophobic	false
N32	N	LEU- 83	2.81	166.08	H-Bond (Protein Donor)	false
N34	O	LEU- 83	2.6	147.83	H-Bond (Ligand Donor)	false
C5	CB	ASN- 132	3.74	0	Hydrophobic	false
C17	CD2	LEU- 134	3.68	0	Hydrophobic	false
C36	CD2	LEU- 134	4.37	0	Hydrophobic	false
C15	CD1	LEU- 134	3.3	0	Hydrophobic	false
C4	CB	ALA- 144	4.09	0	Hydrophobic	false
C21	CB	ALA- 144	3.36	0	Hydrophobic	false
C23	CB	ASP- 145	4.4	0	Hydrophobic	false
C23	CD2	LEU- 148	4.34	0	Hydrophobic	false