scPDB - 1p2a entry

Protein Data Bank Entry:

PDB ID : 1p2a

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2003-04-15

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:	29.031
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.562	654.750

% Hydrophobic	% Polar
42.27	57.73
According to VolSite

Ligand :

HET Code:	5BN
Formula:	C17H16FN4O
Molecular weight:	311.334 g/mol
DrugBank ID:	DB07163
Buried Surface Area:	63.11 %
Polar Surface area:	84.56 Å2

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

Mass center Coordinates

X	Y	Z
13.0983	-8.60243	11.3833

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
C9	CD1	ILE- 10	3.68	0	Hydrophobic	false
C20	CG2	VAL- 18	4.39	0	Hydrophobic	false
C3	CG1	VAL- 18	4.34	0	Hydrophobic	false
F	CG2	VAL- 18	3.99	0	Hydrophobic	false
C4	CG1	VAL- 18	4.01	0	Hydrophobic	false
C1	CB	ALA- 31	3.89	0	Hydrophobic	false
C5	CB	ALA- 31	4.12	0	Hydrophobic	false
C1	CG1	VAL- 64	3.83	0	Hydrophobic	false
C2	CD2	PHE- 80	3.37	0	Hydrophobic	false
C1	CB	PHE- 80	3.32	0	Hydrophobic	false
N12	O	GLU- 81	2.89	170.43	H-Bond (Ligand Donor)	false
N18	O	LEU- 83	3.02	126.69	H-Bond (Ligand Donor)	false
O13	N	LEU- 83	2.76	146.74	H-Bond (Protein Donor)	false
C9	CD2	LEU- 134	3.91	0	Hydrophobic	false
C10	CD1	LEU- 134	3.52	0	Hydrophobic	false
N22	OD2	ASP- 145	3.34	156.2	H-Bond (Ligand Donor)	false
N19	OD2	ASP- 145	3.46	163.07	H-Bond (Ligand Donor)	false
N22	OD2	ASP- 145	3.34	0	Ionic (Ligand Cationic)	false
F	CB	ASP- 145	3.25	0	Hydrophobic	false