scPDB - 2vnw entry

Protein Data Bank Entry:

PDB ID : 2vnw

Resolution :2.090 Å

Experimental Method : X-ray

Deposition Date : 2008-02-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	cAMP-dependent protein kinase catalytic subunit alpha
ID:	KAPCA_BOVIN
AC:	P00517
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	2.7.11.11

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
I	4 %

Ligand binding site composition:

B-Factor:	17.593
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.061	914.625

% Hydrophobic	% Polar
47.23	52.77
According to VolSite

Ligand :

HET Code:	M01
Formula:	C11H17N6
Molecular weight:	233.293 g/mol
DrugBank ID:	-
Buried Surface Area:	77.51 %
Polar Surface area:	85.34 Å2

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

Mass center Coordinates

X	Y	Z
6.46782	9.32641	3.21518

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
C12	CB	LEU- 49	3.92	0	Hydrophobic	false
C14	CG2	VAL- 57	3.88	0	Hydrophobic	false
C12	CG1	VAL- 57	4.03	0	Hydrophobic	false
N9	O	GLU- 121	2.71	154.37	H-Bond (Ligand Donor)	false
N3	N	ALA- 123	2.88	174.12	H-Bond (Protein Donor)	false
C11	CG	GLU- 127	4.36	0	Hydrophobic	false
N10	O	GLU- 170	2.84	130.77	H-Bond (Ligand Donor)	false
N10	OD1	ASN- 171	2.93	120.63	H-Bond (Ligand Donor)	false
C12	CE	MET- 173	4.39	0	Hydrophobic	false
C11	SD	MET- 173	3.87	0	Hydrophobic	false
C15	CB	THR- 183	4.19	0	Hydrophobic	false
N10	OD1	ASP- 184	2.53	155.46	H-Bond (Ligand Donor)	false
N10	OD1	ASP- 184	2.53	0	Ionic (Ligand Cationic)	false
N10	OD2	ASP- 184	3.07	0	Ionic (Ligand Cationic)	false