scPDB - 4bvb entry

Protein Data Bank Entry:

PDB ID : 4bvb

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2013-06-25

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:	14.430
Number of residues:	30
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.346	553.500

% Hydrophobic	% Polar
63.41	36.59
According to VolSite

Ligand :

HET Code:	OCZ
Formula:	C13H13ClN2O
Molecular weight:	248.708 g/mol
DrugBank ID:	-
Buried Surface Area:	75.02 %
Polar Surface area:	58.88 Å2

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

Mass center Coordinates

X	Y	Z
8.47647	-13.5258	3.50282

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
CAK	CB	ALA- 146	4.03	0	Hydrophobic	false
CAM	CG2	ILE- 154	3.88	0	Hydrophobic	false
CAJ	CZ	PHE- 157	3.83	0	Hydrophobic	false
CAF	CZ	PHE- 157	3.44	0	Hydrophobic	false
CAL	CE1	PHE- 157	3.91	0	Hydrophobic	false
CAM	CD1	LEU- 164	3.92	0	Hydrophobic	false
CL	CD1	PHE- 180	3.55	0	Hydrophobic	false
CAJ	CD1	LEU- 199	3.77	0	Hydrophobic	false
NAG	O	GLN- 228	3.32	142.14	H-Bond (Ligand Donor)	false
OAP	N	ILE- 230	2.69	147.42	H-Bond (Protein Donor)	false
CAJ	CD1	ILE- 230	4.12	0	Hydrophobic	false
CAE	CG1	ILE- 230	3.79	0	Hydrophobic	false
CAD	CG2	ILE- 230	3.6	0	Hydrophobic	false
CAA	CD1	ILE- 230	3.53	0	Hydrophobic	false
NAQ	OD2	ASP- 231	2.95	165.28	H-Bond (Ligand Donor)	false
OAP	N	ASP- 231	3.23	123.32	H-Bond (Protein Donor)	false
CAD	CB	HIS- 248	3.81	0	Hydrophobic	false
CL	CG2	ILE- 291	3.42	0	Hydrophobic	false
CAB	CG2	ILE- 291	3.66	0	Hydrophobic	false
CL	CD1	PHE- 293	3.83	0	Hydrophobic	false
CL	CE1	PHE- 294	4.32	0	Hydrophobic	false
NAQ	O	HOH- 2014	2.88	154.56	H-Bond (Ligand Donor)	false