scPDB - 5dc5 entry

Protein Data Bank Entry:

PDB ID : 5dc5

Resolution :1.940 Å

Experimental Method : X-ray

Deposition Date : 2015-08-23

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	23 %
B	77 %

Ligand binding site composition:

B-Factor:	30.489
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.331	2308.500

% Hydrophobic	% Polar
48.98	51.02
According to VolSite

Ligand :

HET Code:	B3N
Formula:	C16H25N3O3
Molecular weight:	307.388 g/mol
DrugBank ID:	DB02565
Buried Surface Area:	63.86 %
Polar Surface area:	81.67 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-16.4802	17.7435	-26.8971

Binding mode :

What is Poseview ?

2D View
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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
C22	CD	LYS- 33	4.29	0	Hydrophobic	false
O4	NE2	HIS- 142	2.54	155.12	H-Bond (Protein Donor)	false
N3	NE2	HIS- 143	2.74	143.98	H-Bond (Ligand Donor)	false
C21	CZ	PHE- 152	3.69	0	Hydrophobic	false
C5	CD1	PHE- 152	3.73	0	Hydrophobic	false
C9	CZ	PHE- 152	3.75	0	Hydrophobic	false
C7	CE1	PHE- 152	3.43	0	Hydrophobic	false
C9	CG	PHE- 208	4.13	0	Hydrophobic	false
C8	CD1	PHE- 208	3.7	0	Hydrophobic	false
C7	CE1	PHE- 208	4.04	0	Hydrophobic	false
C14	CG	PRO- 273	3.68	0	Hydrophobic	false
C21	CE	MET- 274	3.73	0	Hydrophobic	false
C17	CB	TYR- 306	4.38	0	Hydrophobic	false
C22	CD2	TYR- 306	3.67	0	Hydrophobic	false
C21	CD2	TYR- 306	4.08	0	Hydrophobic	false
C5	CZ	TYR- 306	4.38	0	Hydrophobic	false
O2	OH	TYR- 306	2.77	167.54	H-Bond (Protein Donor)	false
O2	ZN	ZN- 401	2.19	0	Metal Acceptor	false
O4	ZN	ZN- 401	2.15	0	Metal Acceptor	false