scPDB - 3agl entry

Protein Data Bank Entry:

PDB ID : 3agl

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2010-04-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.240	8.240	8.240	0.000	8.240	1

List of CHEMBLId :

CHEMBL505949

Binding Site :

Uniprot Annotation

Name:	cAMP-dependent protein kinase catalytic subunit alpha
ID:	KAPCA_HUMAN
AC:	P17612
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.11

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	18.166
Number of residues:	52
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.700	614.250

% Hydrophobic	% Polar
47.80	52.20
According to VolSite

Ligand :

HET Code:	A03
Formula:	C37H65N17O9
Molecular weight:	892.020 g/mol
DrugBank ID:	-
Buried Surface Area:	53.05 %
Polar Surface area:	435.17 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	15
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	30

Mass center Coordinates

X	Y	Z
-19.3297	55.6387	-21.525

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
CCJ	CB	LEU- 49	4.29	0	Hydrophobic	false
O	OG	SER- 53	3.25	158.6	H-Bond (Protein Donor)	false
O	N	SER- 53	3.18	161.6	H-Bond (Protein Donor)	false
OAI	N	PHE- 54	2.93	171.61	H-Bond (Protein Donor)	false
CBD	CE2	PHE- 54	3.63	0	Hydrophobic	false
CB	CE1	PHE- 54	3.85	0	Hydrophobic	false
CCJ	CG1	VAL- 57	4.32	0	Hydrophobic	false
CAU	CG2	VAL- 57	4.47	0	Hydrophobic	false
CBD	CD2	LEU- 74	3.75	0	Hydrophobic	false
N6	O	GLU- 121	2.92	158.02	H-Bond (Ligand Donor)	false
N1	N	VAL- 123	2.97	170.29	H-Bond (Protein Donor)	false
OAO	OE2	GLU- 127	2.7	151.81	H-Bond (Ligand Donor)	false
NAC	OE1	GLU- 127	3.49	135.73	H-Bond (Ligand Donor)	false
NAC	OE2	GLU- 127	2.61	152.41	H-Bond (Ligand Donor)	false
NAE	OE1	GLU- 127	2.99	163.81	H-Bond (Ligand Donor)	false
NAE	OE2	GLU- 127	3.45	122.07	H-Bond (Ligand Donor)	false
CCH	CG	GLU- 127	4.07	0	Hydrophobic	false
CBT	OE1	GLU- 127	3.69	0	Ionic (Ligand Cationic)	false
CBT	OE2	GLU- 127	3.43	0	Ionic (Ligand Cationic)	false
CBF	CZ	PHE- 129	4.34	0	Hydrophobic	false
OAN	O	GLU- 170	2.92	152.08	H-Bond (Ligand Donor)	false
NBK	OE2	GLU- 170	2.81	159.87	H-Bond (Ligand Donor)	false
NAD	OE1	GLU- 170	3.05	172.44	H-Bond (Ligand Donor)	false
CBS	OE1	GLU- 170	3.82	0	Ionic (Ligand Cationic)	false
CBS	OE2	GLU- 170	3.61	0	Ionic (Ligand Cationic)	false
CCH	CD2	LEU- 173	3.88	0	Hydrophobic	false
N7	OG1	THR- 183	3.01	174.87	H-Bond (Protein Donor)	false
CCG	CG2	THR- 183	4.39	0	Hydrophobic	false
CB	CZ	PHE- 187	3.75	0	Hydrophobic	false
CBB	CG2	THR- 201	4.1	0	Hydrophobic	false
CBS	OE1	GLU- 230	3.77	0	Ionic (Ligand Cationic)	false
CBS	OE2	GLU- 230	3.53	0	Ionic (Ligand Cationic)	false
NAB	OE1	GLU- 230	3.44	134.68	H-Bond (Ligand Donor)	false
NAB	OE2	GLU- 230	3.11	139.98	H-Bond (Ligand Donor)	false
NAD	OE1	GLU- 230	3.25	141.01	H-Bond (Ligand Donor)	false
NAD	OE2	GLU- 230	3.09	141.15	H-Bond (Ligand Donor)	false
CCH	CE1	PHE- 327	4.18	0	Hydrophobic	false
OAJ	O	HOH- 375	2.85	157.81	H-Bond (Protein Donor)	false