scPDB - 2gnf entry

Protein Data Bank Entry:

PDB ID : 2gnf

Resolution :2.280 Å

Experimental Method : X-ray

Deposition Date : 2006-04-10

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	86 %
I	14 %

Ligand binding site composition:

B-Factor:	38.550
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.914	1063.125

% Hydrophobic	% Polar
39.68	60.32
According to VolSite

Ligand :

HET Code:	Y27
Formula:	C14H22N3O
Molecular weight:	248.344 g/mol
DrugBank ID:	DB08756
Buried Surface Area:	59.01 %
Polar Surface area:	69.63 Å2

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

Mass center Coordinates

X	Y	Z
8.59956	9.251	43.2554

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
C15	CD1	ILE- 49	3.72	0	Hydrophobic	false
C32	CG2	VAL- 57	3.37	0	Hydrophobic	false
C13	CB	ALA- 70	3.77	0	Hydrophobic	false
C13	SD	MET- 120	4.26	0	Hydrophobic	false
N11	N	MET- 123	3.08	169.36	H-Bond (Protein Donor)	false
C42	CB	GLU- 170	4.27	0	Hydrophobic	false
N43	OD1	ASN- 171	2.77	167.26	H-Bond (Ligand Donor)	false
C15	CD2	LEU- 173	3.59	0	Hydrophobic	false
C13	CD1	LEU- 173	3.62	0	Hydrophobic	false
C36	CB	ALA- 183	4.18	0	Hydrophobic	false
N43	OD1	ASP- 184	2.51	168.22	H-Bond (Ligand Donor)	false
N43	OD1	ASP- 184	2.51	0	Ionic (Ligand Cationic)	false
C34	CB	ASP- 184	4.27	0	Hydrophobic	false