scPDB - 3amb entry

Protein Data Bank Entry:

PDB ID : 3amb

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2010-08-18

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_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
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	23.519
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.099	1501.875

% Hydrophobic	% Polar
41.35	58.65
According to VolSite

Ligand :

HET Code:	VX6
Formula:	C23H29N8OS
Molecular weight:	465.594 g/mol
DrugBank ID:	-
Buried Surface Area:	58.54 %
Polar Surface area:	128.57 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-29.8378	-9.68061	-6.99842

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	CD2	LEU- 49	4.15	0	Hydrophobic	false
S23	CB	LEU- 49	4.07	0	Hydrophobic	false
C29	CB	LEU- 49	4.08	0	Hydrophobic	false
C28	CG1	VAL- 57	3.89	0	Hydrophobic	false
C21	CB	ALA- 70	3.56	0	Hydrophobic	false
C35	CD	LYS- 72	3.55	0	Hydrophobic	false
C21	CD1	LEU- 120	4.19	0	Hydrophobic	false
C34	CD1	LEU- 120	3.63	0	Hydrophobic	false
N19	O	GLU- 121	2.96	162.18	H-Bond (Ligand Donor)	false
N14	O	ALA- 123	2.97	146.75	H-Bond (Ligand Donor)	false
N20	N	ALA- 123	2.79	177.84	H-Bond (Protein Donor)	false
C25	CB	GLU- 127	4.43	0	Hydrophobic	false
C21	CD1	LEU- 173	3.88	0	Hydrophobic	false
C26	CD2	LEU- 173	4.04	0	Hydrophobic	false
C33	CB	ALA- 183	4.12	0	Hydrophobic	false
C33	CB	ASP- 184	3.89	0	Hydrophobic	false
N1	OD1	ASN- 326	2.94	158.55	H-Bond (Ligand Donor)	false
C3	CD1	PHE- 327	3.9	0	Hydrophobic	false
C5	CE1	PHE- 327	3.82	0	Hydrophobic	false