scPDB - 4jt9 entry

Protein Data Bank Entry:

PDB ID : 4jt9

Resolution :2.240 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:	34.450
Number of residues:	31
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.694	999.000

% Hydrophobic	% Polar
36.82	63.18
According to VolSite

Ligand :

HET Code:	1NS
Formula:	C15H21N5O3S2
Molecular weight:	383.489 g/mol
DrugBank ID:	-
Buried Surface Area:	67.69 %
Polar Surface area:	154.9 Å2

Number of
H-Bond Acceptors:	6
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
24.0322	44.0743	-10.0558

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
S18	CZ	PHE- 157	3.68	0	Hydrophobic	false
C23	CD2	PHE- 157	4.2	0	Hydrophobic	false
N19	N	PHE- 157	2.95	175.61	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 157	3.75	0	Aromatic Face/Face	false
C23	CE2	PHE- 180	3.84	0	Hydrophobic	false
C07	CG2	ILE- 230	3.94	0	Hydrophobic	false
S18	CG1	ILE- 230	4.02	0	Hydrophobic	false
O17	N	ILE- 230	2.78	139.45	H-Bond (Protein Donor)	false
N16	OD2	ASP- 231	2.62	144.73	H-Bond (Ligand Donor)	false
O17	N	ASP- 231	2.83	129.18	H-Bond (Protein Donor)	false
C04	CB	HIS- 248	3.89	0	Hydrophobic	false
C07	CB	HIS- 248	3.88	0	Hydrophobic	false
C04	CG2	ILE- 291	4.22	0	Hydrophobic	false
N03	O	VAL- 292	3.04	131.44	H-Bond (Ligand Donor)	false
C01	CE1	PHE- 294	4.36	0	Hydrophobic	false
N16	O	HOH- 522	3.03	167.45	H-Bond (Ligand Donor)	false