scPDB - 4bz7 entry

Protein Data Bank Entry:

PDB ID : 4bz7

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2013-07-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Histone deacetylase
ID:	A5H660_SCHMA
AC:	A5H660
Organism:	Schistosoma mansoni
Reign:	Eukaryota
TaxID:	6183
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	61 %
D	39 %

Ligand binding site composition:

B-Factor:	18.658
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.243	2504.250

% Hydrophobic	% Polar
38.81	61.19
According to VolSite

Ligand :

HET Code:	B3N
Formula:	C16H25N3O3
Molecular weight:	307.388 g/mol
DrugBank ID:	DB02565
Buried Surface Area:	67.38 %
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
57.9893	13.4395	36.1462

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
C22	CG1	VAL- 44	4.22	0	Hydrophobic	false
C22	CG	PRO- 45	4.21	0	Hydrophobic	false
C16	CG	PRO- 45	3.75	0	Hydrophobic	false
C14	CD1	LEU- 47	3.89	0	Hydrophobic	false
O23	N	GLN- 48	2.99	136.7	H-Bond (Protein Donor)	false
C17	CB	TYR- 99	4.45	0	Hydrophobic	false
C22	CD1	TYR- 99	3.93	0	Hydrophobic	false
C21	CD1	TYR- 99	3.62	0	Hydrophobic	false
N12	OD2	ASP- 100	3	145.16	H-Bond (Ligand Donor)	false
C16	CB	ALA- 120	4.43	0	Hydrophobic	false
C22	CB	ALA- 120	3.79	0	Hydrophobic	false
C21	CB	SER- 123	3.81	0	Hydrophobic	false
O4	NE2	HIS- 141	2.69	163.13	H-Bond (Protein Donor)	false
N3	NE2	HIS- 142	2.57	154.78	H-Bond (Ligand Donor)	false
C8	CZ	PHE- 151	4.15	0	Hydrophobic	false
C5	CE2	PHE- 151	3.77	0	Hydrophobic	false
C9	CD1	PHE- 216	3.85	0	Hydrophobic	false
C8	CG	PHE- 216	3.69	0	Hydrophobic	false
C5	CE2	PHE- 216	4.34	0	Hydrophobic	false
C7	CD2	PHE- 216	3.65	0	Hydrophobic	false
O2	ZN	ZN- 500	2.35	0	Metal Acceptor	false
O4	ZN	ZN- 500	2.04	0	Metal Acceptor	false