scPDB - 2vcg entry

Protein Data Bank Entry:

PDB ID : 2vcg

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-09-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Histone deacetylase-like amidohydrolase
ID:	HDAH_ALCSD
AC:	Q70I53
Organism:	Alcaligenes sp. )
Reign:	Bacteria
TaxID:	242601
EC Number:	3.5.1

Chains:

Chain Name:	Percentage of Residues within binding site
B	15 %
C	85 %

Ligand binding site composition:

B-Factor:	15.884
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.465	408.375

% Hydrophobic	% Polar
73.55	26.45
According to VolSite

Ligand :

HET Code:	S17
Formula:	C18H25BrN2O5
Molecular weight:	429.305 g/mol
DrugBank ID:	DB08505
Buried Surface Area:	66.57 %
Polar Surface area:	104.73 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-1.35762	19.6626	-7.88138

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
CB	CB	ALA- 28	4.26	0	Hydrophobic	false
CAA	CB	ALA- 28	3.72	0	Hydrophobic	false
CAA	CE	MET- 36	4.14	0	Hydrophobic	false
CB	CG2	ILE- 106	4.17	0	Hydrophobic	false
CAP	CD1	ILE- 106	3.51	0	Hydrophobic	false
NAR	NE2	HIS- 149	2.6	139.55	H-Bond (Ligand Donor)	false
CAN	CZ	PHE- 158	3.65	0	Hydrophobic	false
CAO	CE1	PHE- 158	3.71	0	Hydrophobic	false
CAP	CE2	PHE- 214	3.86	0	Hydrophobic	false
CAL	CE1	PHE- 214	4.12	0	Hydrophobic	false
CAK	CG	PHE- 214	4.49	0	Hydrophobic	false
CAM	CD1	PHE- 214	3.88	0	Hydrophobic	false
BR1	CG	PRO- 216	4.07	0	Hydrophobic	false
CAK	CD1	LEU- 281	3.78	0	Hydrophobic	false
CAO	CZ	TYR- 318	4.12	0	Hydrophobic	false
CAA	CD1	TYR- 344	3.59	0	Hydrophobic	false
CE1	CB	GLU- 346	4.24	0	Hydrophobic	false
BR1	CG	GLU- 346	4.14	0	Hydrophobic	false
CAP	CE1	PHE- 347	3.28	0	Hydrophobic	false
CE1	CB	PHE- 347	3.79	0	Hydrophobic	false
OAB	ZN	ZN- 1377	2.19	0	Metal Acceptor	false
OAE	ZN	ZN- 1377	2.06	0	Metal Acceptor	false