scPDB - 2xnb entry

Protein Data Bank Entry:

PDB ID : 2xnb

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2010-08-01

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:	52.220
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.897	445.500

% Hydrophobic	% Polar
49.24	50.76
According to VolSite

Ligand :

HET Code:	Y8L
Formula:	C19H23N6OS
Molecular weight:	383.491 g/mol
DrugBank ID:	-
Buried Surface Area:	57.41 %
Polar Surface area:	103.6 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	4
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
25.036	27.7551	27.4375

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
C27	CG1	ILE- 10	4.29	0	Hydrophobic	false
C9	CD1	ILE- 10	3.52	0	Hydrophobic	false
C12	CB	ILE- 10	3.91	0	Hydrophobic	false
S23	CG1	VAL- 18	4.26	0	Hydrophobic	false
C29	CB	VAL- 18	4.15	0	Hydrophobic	false
C27	CB	VAL- 18	4.26	0	Hydrophobic	false
C1	CB	ALA- 31	3.31	0	Hydrophobic	false
O28	NZ	LYS- 33	2.84	173.17	H-Bond (Protein Donor)	false
C1	CG1	VAL- 64	4.17	0	Hydrophobic	false
C1	CB	PHE- 80	4.19	0	Hydrophobic	false
S23	CD2	PHE- 80	3.83	0	Hydrophobic	false
N7	O	LEU- 83	2.9	162.98	H-Bond (Ligand Donor)	false
N3	N	LEU- 83	3.15	168.12	H-Bond (Protein Donor)	false
C13	CB	ASP- 86	4.47	0	Hydrophobic	false
C14	CD1	LEU- 134	3.4	0	Hydrophobic	false
S23	CB	ALA- 144	4.36	0	Hydrophobic	false