scPDB - 2x1n entry

Protein Data Bank Entry:

PDB ID : 2x1n

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2009-12-31

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
C	100 %

Ligand binding site composition:

B-Factor:	43.282
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.196	553.500

% Hydrophobic	% Polar
51.83	48.17
According to VolSite

Ligand :

HET Code:	X1N
Formula:	C16H13N5O2S
Molecular weight:	339.372 g/mol
DrugBank ID:	-
Buried Surface Area:	60.15 %
Polar Surface area:	125.08 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
46.395	48.0073	24.2674

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
C1B	CD1	ILE- 10	4.1	0	Hydrophobic	false
C5B	CB	ILE- 10	4	0	Hydrophobic	false
S4A	CG2	VAL- 18	4.47	0	Hydrophobic	false
C20	CG2	VAL- 18	4.3	0	Hydrophobic	false
C5	CB	ALA- 31	3.74	0	Hydrophobic	false
C60	CG1	VAL- 64	4.33	0	Hydrophobic	false
C6A	CD1	PHE- 80	4.07	0	Hydrophobic	false
C60	CB	PHE- 80	3.72	0	Hydrophobic	false
N7	O	LEU- 83	2.64	161.43	H-Bond (Ligand Donor)	false
N1	N	LEU- 83	3.14	160.94	H-Bond (Protein Donor)	false
C4B	CB	GLN- 85	4.3	0	Hydrophobic	false
C2B	CD2	LEU- 134	4.31	0	Hydrophobic	false
C5	CD1	LEU- 134	3.46	0	Hydrophobic	false