scPDB - 4bgh entry

Protein Data Bank Entry:

PDB ID : 4bgh

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2013-03-26

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:	32.731
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.427	641.250

% Hydrophobic	% Polar
43.16	56.84
According to VolSite

Ligand :

HET Code:	3I6
Formula:	C13H16BrN5O3S
Molecular weight:	402.267 g/mol
DrugBank ID:	-
Buried Surface Area:	65.44 %
Polar Surface area:	138.6 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
10.6192	-9.29674	11.0593

Binding mode :

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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
C15	CG1	ILE- 10	4.22	0	Hydrophobic	false
C2	CD1	ILE- 10	3.89	0	Hydrophobic	false
C15	CG1	VAL- 18	3.92	0	Hydrophobic	false
C8	CB	ALA- 31	3.55	0	Hydrophobic	false
BR1	CG1	VAL- 64	3.97	0	Hydrophobic	false
BR1	CB	PHE- 80	3.56	0	Hydrophobic	false
N12	N	LEU- 83	3.04	171.86	H-Bond (Protein Donor)	false
N1	O	LEU- 83	2.73	152.24	H-Bond (Ligand Donor)	false
O2	N	ASP- 86	2.94	169.77	H-Bond (Protein Donor)	false
N4	OD2	ASP- 86	2.93	169.25	H-Bond (Ligand Donor)	false
C6	CB	ASP- 86	3.97	0	Hydrophobic	false
C13	CD2	LEU- 134	4.25	0	Hydrophobic	false
C8	CD1	LEU- 134	3.42	0	Hydrophobic	false
C1	CD2	LEU- 134	3.84	0	Hydrophobic	false
C14	CB	ALA- 144	4.39	0	Hydrophobic	false
BR1	CB	ALA- 144	4.29	0	Hydrophobic	false