scPDB - 3r7e entry

Protein Data Bank Entry:

PDB ID : 3r7e

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-03-22

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:	28.850
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.916	516.375

% Hydrophobic	% Polar
48.37	51.63
According to VolSite

Ligand :

HET Code:	X88
Formula:	C12H11N5O3
Molecular weight:	273.247 g/mol
DrugBank ID:	-
Buried Surface Area:	49.76 %
Polar Surface area:	126.71 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
65.308	46.3267	-47.1101

Binding mode :

What is Poseview ?

2D View
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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
C1	CG2	ILE- 10	3.52	0	Hydrophobic	false
C4	CG1	VAL- 18	4.12	0	Hydrophobic	false
C4	CB	ALA- 31	3.99	0	Hydrophobic	false
O12	NZ	LYS- 33	3.92	0	Ionic (Protein Cationic)	false
O13	NZ	LYS- 33	3.95	0	Ionic (Protein Cationic)	false
N9	O	GLU- 81	3.07	173.06	H-Bond (Ligand Donor)	false
N7	O	LEU- 83	2.96	128.3	H-Bond (Ligand Donor)	false
O10	N	LEU- 83	2.87	172.62	H-Bond (Protein Donor)	false
C1	CD2	LEU- 134	4.26	0	Hydrophobic	false
C14	CD2	LEU- 134	3.86	0	Hydrophobic	false
C5	CD1	LEU- 134	3.69	0	Hydrophobic	false
N19	O	HOH- 366	2.89	179.95	H-Bond (Protein Donor)	false