scPDB - 2v5x entry

Protein Data Bank Entry:

PDB ID : 2v5x

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2007-07-10

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	27 %
B	73 %

Ligand binding site composition:

B-Factor:	34.483
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.715	1809.000

% Hydrophobic	% Polar
48.69	51.31
According to VolSite

Ligand :

HET Code:	V5X
Formula:	C36H41N5O5
Molecular weight:	623.741 g/mol
DrugBank ID:	-
Buried Surface Area:	48.89 %
Polar Surface area:	148.33 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	6
Rings:	5
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
17.9487	-6.4815	52.8962

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
NAH	O	LYS- 33	3.08	144.42	H-Bond (Ligand Donor)	false
CAD	CG	PRO- 35	3.89	0	Hydrophobic	false
CBI	CB	TYR- 100	4	0	Hydrophobic	false
N	OD2	ASP- 101	3.11	143.03	H-Bond (Ligand Donor)	false
NAR	OD1	ASP- 101	3.19	167.49	H-Bond (Ligand Donor)	false
OBB	NE2	HIS- 142	2.68	167.62	H-Bond (Protein Donor)	false
NBA	NE2	HIS- 143	2.79	145.38	H-Bond (Ligand Donor)	false
CAV	CZ	PHE- 152	4.05	0	Hydrophobic	false
CAY	CD1	PHE- 152	3.57	0	Hydrophobic	false
CAX	CE1	PHE- 152	3.65	0	Hydrophobic	false
CB	CB	PHE- 208	3.25	0	Hydrophobic	false
CAV	CG	PHE- 208	4.07	0	Hydrophobic	false
CBM	CB	PHE- 208	4.26	0	Hydrophobic	false
CAW	CD1	PHE- 208	3.46	0	Hydrophobic	false
CAP	CG	PRO- 273	4.11	0	Hydrophobic	false
CAN	CG	PRO- 273	4.25	0	Hydrophobic	false
CAY	CZ	TYR- 306	4.41	0	Hydrophobic	false
CAI	CB	TYR- 306	4.09	0	Hydrophobic	false
OBE	OH	TYR- 306	2.54	164.09	H-Bond (Protein Donor)	false
CAB	CG	LEU- 308	4.34	0	Hydrophobic	false
OBE	ZN	ZN- 1377	2.29	0	Metal Acceptor	false
OBB	ZN	ZN- 1377	2.16	0	Metal Acceptor	false