scPDB - 1t69 entry

Protein Data Bank Entry:

PDB ID : 1t69

Resolution :2.910 Å

Experimental Method : X-ray

Deposition Date : 2004-05-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.540	6.320	6.320	0.330	6.760	10

List of CHEMBLId :

CHEMBL98

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:	61.504
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.793	442.125

% Hydrophobic	% Polar
55.73	44.27
According to VolSite

Ligand :

HET Code:	SHH
Formula:	C14H20N2O3
Molecular weight:	264.320 g/mol
DrugBank ID:	DB02546
Buried Surface Area:	53.93 %
Polar Surface area:	78.42 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
30.1336	-3.17663	-13.8362

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
O1	NE2	HIS- 142	2.68	155.59	H-Bond (Protein Donor)	false
C2	CD2	PHE- 152	3.86	0	Hydrophobic	false
C3	CE2	PHE- 152	3.41	0	Hydrophobic	false
C7	CZ	PHE- 152	4.17	0	Hydrophobic	false
C6	CG	PHE- 208	3.99	0	Hydrophobic	false
C5	CD1	PHE- 208	3.52	0	Hydrophobic	false
C7	CE	MET- 274	3.87	0	Hydrophobic	false
C3	CZ	TYR- 306	4.41	0	Hydrophobic	false
O1	ZN	ZN- 378	1.95	0	Metal Acceptor	false
O2	ZN	ZN- 378	1.98	0	Metal Acceptor	false