scPDB - 1vkg entry

Protein Data Bank Entry:

PDB ID : 1vkg

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2004-05-13

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	23 %
B	77 %

Ligand binding site composition:

B-Factor:	36.872
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.628	1822.500

% Hydrophobic	% Polar
48.70	51.30
According to VolSite

Ligand :

HET Code:	CRI
Formula:	C24H23N3O4
Molecular weight:	417.457 g/mol
DrugBank ID:	DB07586
Buried Surface Area:	44.13 %
Polar Surface area:	98.74 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
13.2759	65.8161	79.6453

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
OH	NE2	HIS- 142	2.81	123.74	H-Bond (Protein Donor)	false
C12	CE1	PHE- 152	3.43	0	Hydrophobic	false
C16	CB	PHE- 208	4.47	0	Hydrophobic	false
C40	CB	PRO- 273	4.49	0	Hydrophobic	false
C14	CG	PRO- 273	3.46	0	Hydrophobic	false
C1	SD	MET- 274	4.19	0	Hydrophobic	false
C6	CE	MET- 274	4.34	0	Hydrophobic	false
C35	CE	MET- 274	3.81	0	Hydrophobic	false
C45	CZ	TYR- 306	3.89	0	Hydrophobic	false
C39	CB	TYR- 306	4.08	0	Hydrophobic	false
OH	ZN	ZN- 400	1.97	0	Metal Acceptor	false
O	ZN	ZN- 400	1.91	0	Metal Acceptor	false