scPDB - 3lfq entry

Protein Data Bank Entry:

PDB ID : 3lfq

Resolution :2.030 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:	20.827
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.024	840.375

% Hydrophobic	% Polar
44.18	55.82
According to VolSite

Ligand :

HET Code:	A28
Formula:	C17H15F2N3O
Molecular weight:	315.317 g/mol
DrugBank ID:	-
Buried Surface Area:	62.8 %
Polar Surface area:	57.78 Å2

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

Mass center Coordinates

X	Y	Z
41.2817	-9.46252	24.9076

Binding mode :

What is Poseview ?

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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
C20	CD1	ILE- 10	4.27	0	Hydrophobic	false
C4	CG1	VAL- 18	4.43	0	Hydrophobic	false
C11	CG2	VAL- 18	3.86	0	Hydrophobic	false
C3	CB	ALA- 31	4.08	0	Hydrophobic	false
C9	CB	ALA- 31	3.59	0	Hydrophobic	false
F17	CG1	VAL- 64	3.38	0	Hydrophobic	false
C3	CB	PHE- 80	4.12	0	Hydrophobic	false
F16	CD2	PHE- 80	3.98	0	Hydrophobic	false
F17	CD2	PHE- 80	3.39	0	Hydrophobic	false
N5	O	GLU- 81	2.89	168.82	H-Bond (Ligand Donor)	false
N6	N	LEU- 83	3.26	160.47	H-Bond (Protein Donor)	false
N18	O	LEU- 83	2.99	170.04	H-Bond (Ligand Donor)	false
C22	CB	ASP- 86	4.32	0	Hydrophobic	false
C14	CB	ASN- 132	3.9	0	Hydrophobic	false
C15	CD2	LEU- 134	4.44	0	Hydrophobic	false
C9	CD1	LEU- 134	3.41	0	Hydrophobic	false
C15	CB	ALA- 144	4.3	0	Hydrophobic	false
F16	CB	ALA- 144	3.64	0	Hydrophobic	false