scPDB - 3sff entry

Protein Data Bank Entry:

PDB ID : 3sff

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2011-06-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Histone deacetylase 8
ID:	HDAC8_HUMAN
AC:	Q9BY41
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.5.1.98

Chains:

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

Ligand binding site composition:

B-Factor:	20.430
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.697	293.625

% Hydrophobic	% Polar
62.07	37.93
According to VolSite

Ligand :

HET Code:	0DI
Formula:	C20H21ClF2N3O2
Molecular weight:	408.849 g/mol
DrugBank ID:	-
Buried Surface Area:	63.7 %
Polar Surface area:	68.26 Å2

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

Mass center Coordinates

X	Y	Z
9.60343	13.7294	-24.0639

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
CL1	CG2	ILE- 34	3.76	0	Hydrophobic	false
CL1	CH2	TRP- 141	3.72	0	Hydrophobic	false
C12	CB	TRP- 141	4.44	0	Hydrophobic	false
DuAr	DuAr	TRP- 141	3.88	0	Aromatic Face/Face	false
N3	NE2	HIS- 142	2.9	160.67	H-Bond (Ligand Donor)	false
F1	CE1	PHE- 152	4.09	0	Hydrophobic	false
C13	SG	CYS- 153	3.8	0	Hydrophobic	false
C6	CB	HIS- 180	4.49	0	Hydrophobic	false
C17	CD2	PHE- 208	3.42	0	Hydrophobic	false
F2	CB	PHE- 208	3.47	0	Hydrophobic	false
CL1	CE2	TYR- 306	3.9	0	Hydrophobic	false
O1	ZN	ZN- 403	2.76	0	Metal Acceptor	false