scPDB - 4nj3 entry

Protein Data Bank Entry:

PDB ID : 4nj3

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2013-11-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.520	6.630	6.520	0.160	6.850	3

List of CHEMBLId :

CHEMBL3099755

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:	38.217
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.638	702.000

% Hydrophobic	% Polar
39.42	60.58
According to VolSite

Ligand :

HET Code:	2KD
Formula:	C27H20ClN2O6
Molecular weight:	503.910 g/mol
DrugBank ID:	-
Buried Surface Area:	71.32 %
Polar Surface area:	128.65 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	4
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-3.58117	32.8829	12.4197

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
C34	CD1	ILE- 10	4.21	0	Hydrophobic	false
C17	CG1	VAL- 18	3.43	0	Hydrophobic	false
C31	CB	ALA- 31	3.4	0	Hydrophobic	false
C03	CD	LYS- 33	4.37	0	Hydrophobic	false
O14	NZ	LYS- 33	3.16	158.26	H-Bond (Protein Donor)	false
CL	CD2	LEU- 55	3.58	0	Hydrophobic	false
C27	CB	LEU- 55	3.79	0	Hydrophobic	false
C27	CD2	LEU- 58	3.69	0	Hydrophobic	false
C28	CG2	ILE- 63	4.11	0	Hydrophobic	false
C09	CB	VAL- 64	4.17	0	Hydrophobic	false
C10	CG1	VAL- 64	3.96	0	Hydrophobic	false
C31	CG1	VAL- 64	4.27	0	Hydrophobic	false
C29	CB	LEU- 66	3.84	0	Hydrophobic	false
C05	CE1	PHE- 80	3.36	0	Hydrophobic	false
C31	CB	PHE- 80	3.7	0	Hydrophobic	false
DuAr	DuAr	PHE- 80	3.9	0	Aromatic Face/Face	false
O36	O	GLU- 81	2.59	140.87	H-Bond (Ligand Donor)	false
O36	N	LEU- 83	3.01	133.43	H-Bond (Protein Donor)	false
CL	CG1	VAL- 123	3.83	0	Hydrophobic	false
C22	CD2	LEU- 134	3.93	0	Hydrophobic	false
C32	CD1	LEU- 134	3.39	0	Hydrophobic	false
C10	CB	ALA- 144	4.12	0	Hydrophobic	false
N01	N	ASP- 145	3.02	144.67	H-Bond (Protein Donor)	false
C03	CB	ASP- 145	3.79	0	Hydrophobic	false
C07	CB	PHE- 146	4.23	0	Hydrophobic	false
C25	CB	PHE- 146	3.86	0	Hydrophobic	false
CL	CD1	PHE- 146	3.88	0	Hydrophobic	false
C25	CD2	PHE- 146	3.36	0	Hydrophobic	false
C07	CG	LEU- 148	4.15	0	Hydrophobic	false
C25	CD1	LEU- 148	3.53	0	Hydrophobic	false
O24	N	LEU- 148	2.63	169.93	H-Bond (Protein Donor)	false