scPDB - 3ig7 entry

Protein Data Bank Entry:

PDB ID : 3ig7

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2009-07-27

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:	39.225
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.513	604.125

% Hydrophobic	% Polar
43.58	56.42
According to VolSite

Ligand :

HET Code:	EFP
Formula:	C18H22N4O3
Molecular weight:	342.392 g/mol
DrugBank ID:	-
Buried Surface Area:	59.89 %
Polar Surface area:	85.25 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
1.40136	28.2037	7.52952

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
C13	CG2	ILE- 10	3.51	0	Hydrophobic	false
C24	CG2	ILE- 10	3.51	0	Hydrophobic	false
C40	CG2	VAL- 18	4.31	0	Hydrophobic	false
C45	CG1	VAL- 18	3.74	0	Hydrophobic	false
C45	CB	ALA- 31	3.62	0	Hydrophobic	false
C40	CD	LYS- 33	4.26	0	Hydrophobic	false
O44	NZ	LYS- 33	3.12	133.75	H-Bond (Protein Donor)	false
C1	CB	PHE- 80	3.92	0	Hydrophobic	false
C32	CD1	PHE- 80	4.45	0	Hydrophobic	false
C45	CD1	PHE- 80	3.95	0	Hydrophobic	false
N7	O	LEU- 83	2.71	176.15	H-Bond (Ligand Donor)	false
N29	N	LEU- 83	2.8	167.51	H-Bond (Protein Donor)	false
C10	CB	ASP- 86	4.48	0	Hydrophobic	false
C32	CD1	LEU- 134	4.07	0	Hydrophobic	false
C32	CB	ALA- 144	3.75	0	Hydrophobic	false