scPDB - 4jt8 entry

Protein Data Bank Entry:

PDB ID : 4jt8

Resolution :2.260 Å

Experimental Method : X-ray

Deposition Date : 2013-03-22

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:	40.234
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.597	675.000

% Hydrophobic	% Polar
41.00	59.00
According to VolSite

Ligand :

HET Code:	1NR
Formula:	C19H27N5O2S
Molecular weight:	389.515 g/mol
DrugBank ID:	-
Buried Surface Area:	64.56 %
Polar Surface area:	129.45 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
23.2351	42.667	-10.6619

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
N3	N	PHE- 157	2.96	175.25	H-Bond (Protein Donor)	false
SAT	CZ	PHE- 157	3.75	0	Hydrophobic	false
CAH	CD2	PHE- 157	4.29	0	Hydrophobic	false
DuAr	DuAr	PHE- 157	3.66	0	Aromatic Face/Face	false
CAE	CD2	PHE- 180	3.87	0	Hydrophobic	false
CAG	CE2	PHE- 180	3.98	0	Hydrophobic	false
CAK	CG2	ILE- 230	3.79	0	Hydrophobic	false
SAT	CG1	ILE- 230	4.01	0	Hydrophobic	false
OAV	N	ILE- 230	2.69	133.9	H-Bond (Protein Donor)	false
OAV	N	ASP- 231	2.92	135.41	H-Bond (Protein Donor)	false
NAW	OD2	ASP- 231	2.88	151.52	H-Bond (Ligand Donor)	false
CAK	CB	HIS- 248	3.98	0	Hydrophobic	false
CAE	CG2	ILE- 291	4.41	0	Hydrophobic	false
CBA	CG1	VAL- 292	3.48	0	Hydrophobic	false
NAB	O	VAL- 292	2.83	141.3	H-Bond (Ligand Donor)	false
CAY	CD1	PHE- 294	3.56	0	Hydrophobic	false
NAW	O	HOH- 502	3.05	159.09	H-Bond (Ligand Donor)	false