scPDB - 2c4g entry

Protein Data Bank Entry:

PDB ID : 2c4g

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2005-10-19

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:	62.711
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.633	567.000

% Hydrophobic	% Polar
43.45	56.55
According to VolSite

Ligand :

HET Code:	514
Formula:	C14H12N4O2
Molecular weight:	268.271 g/mol
DrugBank ID:	-
Buried Surface Area:	61.94 %
Polar Surface area:	75.84 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
-13.775	214.293	104.004

Binding mode :

What is Poseview ?

2D View
3D View

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
C5	CG2	ILE- 10	3.58	0	Hydrophobic	false
O1	NZ	LYS- 33	3.12	165.99	H-Bond (Protein Donor)	false
N3	O	GLU- 81	2.96	168.93	H-Bond (Ligand Donor)	false
N4	N	LEU- 83	3.03	167.24	H-Bond (Protein Donor)	false
N12	O	LEU- 83	3.04	151.8	H-Bond (Ligand Donor)	false
C10	CG	GLN- 85	4.21	0	Hydrophobic	false
C13	CB	GLN- 85	4.38	0	Hydrophobic	false
C7	CB	ASP- 86	4.08	0	Hydrophobic	false
C10	CD	LYS- 89	3.68	0	Hydrophobic	false
O1	O	HOH- 2019	2.77	166.48	H-Bond (Protein Donor)	false