scPDB - 3r8v entry

Protein Data Bank Entry:

PDB ID : 3r8v

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-03-24

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:	22.683
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.244	1167.750

% Hydrophobic	% Polar
43.93	56.07
According to VolSite

Ligand :

HET Code:	Z62
Formula:	C13H12N4O3S
Molecular weight:	304.324 g/mol
DrugBank ID:	-
Buried Surface Area:	69.47 %
Polar Surface area:	142.07 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:	6

Mass center Coordinates

X	Y	Z
-66.2163	-80	-84.009

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
S13	CG2	ILE- 10	4.17	0	Hydrophobic	false
C18	CG2	ILE- 10	3.83	0	Hydrophobic	false
C7	CG1	VAL- 18	3.9	0	Hydrophobic	false
O12	NZ	LYS- 33	2.82	149.37	H-Bond (Protein Donor)	false
DuAr	NZ	LYS- 33	3.9	37.52	Pi/Cation	false
N3	O	GLU- 81	2.87	155.96	H-Bond (Ligand Donor)	false
C16	CE2	PHE- 82	3.63	0	Hydrophobic	false
N1	N	LEU- 83	3.18	170.9	H-Bond (Protein Donor)	false
N15	O	LEU- 83	2.76	139.37	H-Bond (Ligand Donor)	false
C18	CB	ASP- 86	4.14	0	Hydrophobic	false
C10	CB	ASN- 132	3.95	0	Hydrophobic	false
C6	CD1	LEU- 134	4.49	0	Hydrophobic	false
S13	CD2	LEU- 134	4.09	0	Hydrophobic	false
C11	CB	ALA- 144	4.36	0	Hydrophobic	false