scPDB - 2jdt entry

Protein Data Bank Entry:

PDB ID : 2jdt

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2007-01-12

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	91 %
I	9 %

Ligand binding site composition:

B-Factor:	33.007
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.102	847.125

% Hydrophobic	% Polar
45.42	54.58
According to VolSite

Ligand :

HET Code:	I5S
Formula:	C20H23ClN3O3S
Molecular weight:	420.933 g/mol
DrugBank ID:	DB07947
Buried Surface Area:	67.75 %
Polar Surface area:	93.28 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
9.90025	10.33	2.83396

Binding mode :

What is Poseview ?

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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
C27	CD1	LEU- 49	3.99	0	Hydrophobic	false
C20	CG2	VAL- 57	4.29	0	Hydrophobic	false
C3	CG2	VAL- 57	3.75	0	Hydrophobic	false
C19	CG1	VAL- 57	3.91	0	Hydrophobic	false
C23	CB	ALA- 70	3.46	0	Hydrophobic	false
C28	CB	ALA- 70	3.87	0	Hydrophobic	false
CL1	CD	LYS- 72	3.96	0	Hydrophobic	false
CL1	CD2	LEU- 74	3.77	0	Hydrophobic	false
C21	CE	MET- 120	3.5	0	Hydrophobic	false
N25	N	ALA- 123	3.07	172.91	H-Bond (Protein Donor)	false
C14	CG	GLU- 127	4.38	0	Hydrophobic	false
N15	OE2	GLU- 127	3.42	130.59	H-Bond (Ligand Donor)	false
C14	SD	MET- 173	3.93	0	Hydrophobic	false
C27	CE	MET- 173	3.76	0	Hydrophobic	false
C28	SD	MET- 173	4.39	0	Hydrophobic	false
C21	CB	THR- 183	3.79	0	Hydrophobic	false
C22	CG2	THR- 183	3.99	0	Hydrophobic	false
N10	OD2	ASP- 184	2.9	0	Ionic (Ligand Cationic)	false
N10	OD1	ASP- 184	3.81	0	Ionic (Ligand Cationic)	false
O18	O	HOH- 2143	3.09	160.33	H-Bond (Protein Donor)	false