scPDB - 1pkd entry

Protein Data Bank Entry:

PDB ID : 1pkd

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2003-06-05

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:	37.241
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.051	556.875

% Hydrophobic	% Polar
50.30	49.70
According to VolSite

Ligand :

HET Code:	UCN
Formula:	C28H27N4O4
Molecular weight:	483.538 g/mol
DrugBank ID:	DB01933
Buried Surface Area:	67.53 %
Polar Surface area:	94.26 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	8
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-3.43319	50.0383	105.842

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
C1	CB	ILE- 10	4.3	0	Hydrophobic	false
C6	CD1	ILE- 10	3.74	0	Hydrophobic	false
C5	CD1	ILE- 10	3.49	0	Hydrophobic	false
C26	CG2	VAL- 18	3.82	0	Hydrophobic	false
C17	CG2	VAL- 18	3.67	0	Hydrophobic	false
C11	CG1	VAL- 18	3.92	0	Hydrophobic	false
C7	CB	ALA- 31	3.88	0	Hydrophobic	false
C15	CD	LYS- 33	3.67	0	Hydrophobic	false
N1	O	GLU- 81	2.79	158.79	H-Bond (Ligand Donor)	false
O5	N	LEU- 83	2.78	172.79	H-Bond (Protein Donor)	false
N4	O	GLN- 131	2.99	126.71	H-Bond (Ligand Donor)	false
C27	CD2	LEU- 134	4.1	0	Hydrophobic	false
C5	CD2	LEU- 134	4.19	0	Hydrophobic	false
C7	CD1	LEU- 134	3.36	0	Hydrophobic	false
C27	CB	ALA- 144	4.2	0	Hydrophobic	false
C27	CB	ASP- 145	4.46	0	Hydrophobic	false
C15	CB	ASP- 145	3.85	0	Hydrophobic	false