scPDB - 3glu entry

Protein Data Bank Entry:

PDB ID : 3glu

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2009-03-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD-dependent protein deacetylase sirtuin-3, mitochondrial
ID:	SIR3_HUMAN
AC:	Q9NTG7
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.5.1

Chains:

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

Ligand binding site composition:

B-Factor:	40.490
Number of residues:	17
Including
Standard Amino Acids:	17
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.050	870.750

% Hydrophobic	% Polar
50.39	49.61
According to VolSite

Ligand :

HET Code:	LYS_VAL_MET
Formula:	C16H34N4O3S
Molecular weight:	362.531 g/mol
DrugBank ID:	-
Buried Surface Area:	33.19 %
Polar Surface area:	155.85 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-26.2682	-28.3684	-22.1528

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
NZ	O	VAL- 292	2.89	150.43	H-Bond (Ligand Donor)	false
CD	CG1	VAL- 292	3.42	0	Hydrophobic	false
CB	CE1	PHE- 294	3.57	0	Hydrophobic	false
CG	CD1	PHE- 294	4.19	0	Hydrophobic	false
O	N	GLY- 295	2.54	159.05	H-Bond (Protein Donor)	false
N	O	GLU- 296	2.76	158.13	H-Bond (Ligand Donor)	false
CB	CD1	LEU- 298	3.87	0	Hydrophobic	false
CG	CG1	VAL- 324	4.28	0	Hydrophobic	false
N	O	GLU- 325	3.42	162.33	H-Bond (Ligand Donor)	false
O	N	GLU- 325	3.28	156.73	H-Bond (Protein Donor)	false
CG2	CB	GLU- 325	4.06	0	Hydrophobic	false