scPDB - 3ubd entry

Protein Data Bank Entry:

PDB ID : 3ubd

Resolution :1.530 Å

Experimental Method : X-ray

Deposition Date : 2011-10-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribosomal protein S6 kinase alpha-3
ID:	KS6A3_MOUSE
AC:	P18654
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	2.7.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	24.369
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.623	408.375

% Hydrophobic	% Polar
73.55	26.45
According to VolSite

Ligand :

HET Code:	SL0
Formula:	C25H23O12
Molecular weight:	515.443 g/mol
DrugBank ID:	-
Buried Surface Area:	62.38 %
Polar Surface area:	181.1 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	3
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
33.2298	4.48157	8.76603

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
C7	CD1	ILE- 50	3.67	0	Hydrophobic	false
C9	CD1	ILE- 52	4.17	0	Hydrophobic	false
C10	CB	PHE- 79	4.37	0	Hydrophobic	false
C23	CB	ALA- 98	3.98	0	Hydrophobic	false
C10	CD	LYS- 100	3.99	0	Hydrophobic	false
C9	CD1	LEU- 102	4.24	0	Hydrophobic	false
C21	CG2	VAL- 131	4.02	0	Hydrophobic	false
C22	CB	VAL- 131	4.39	0	Hydrophobic	false
C9	CD1	LEU- 145	3.8	0	Hydrophobic	false
C21	CD2	LEU- 147	4.31	0	Hydrophobic	false
C23	CB	LEU- 147	3.62	0	Hydrophobic	false
C24	CD1	LEU- 147	3.78	0	Hydrophobic	false
O11	O	ASP- 148	2.6	155.36	H-Bond (Ligand Donor)	false
C21	CD2	LEU- 150	4.41	0	Hydrophobic	false
C22	CB	LEU- 150	4.05	0	Hydrophobic	false
C18	CD1	LEU- 155	3.92	0	Hydrophobic	false
O9	O	GLU- 197	2.63	149	H-Bond (Ligand Donor)	false
C15	CD1	LEU- 200	3.87	0	Hydrophobic	false
C21	CD1	LEU- 200	3.85	0	Hydrophobic	false
C18	CD2	LEU- 200	3.9	0	Hydrophobic	false
C15	CG2	THR- 210	4.13	0	Hydrophobic	false
C7	CD2	LEU- 214	4.18	0	Hydrophobic	false
C9	CD2	LEU- 214	4.25	0	Hydrophobic	false
C16	CD2	LEU- 214	3.7	0	Hydrophobic	false
O12	O	HOH- 530	2.9	180	H-Bond (Protein Donor)	false