scPDB - 3znr entry

Protein Data Bank Entry:

PDB ID : 3znr

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2013-02-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Histone deacetylase 7
ID:	HDAC7_HUMAN
AC:	Q8WUI4
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.5.1.98

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	22.674
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.744	317.250

% Hydrophobic	% Polar
67.02	32.98
According to VolSite

Ligand :

HET Code:	NU9
Formula:	C25H21F3N4O3S
Molecular weight:	514.519 g/mol
DrugBank ID:	-
Buried Surface Area:	61.48 %
Polar Surface area:	118.38 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-6.49769	2.77508	-15.65

Binding mode :

What is Poseview ?

2D View
3D View

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
O09	ZN	ZN- 101	2.68	0	Metal Acceptor	false
DuAr	ZN	ZN- 101	3.17	144.94	Pi/Cation	false
S30	CG	PRO- 542	3.91	0	Hydrophobic	false
C31	CG	PRO- 542	3.69	0	Hydrophobic	false
C36	CB	PRO- 542	3.63	0	Hydrophobic	false
C33	CB	GLU- 543	4.3	0	Hydrophobic	false
C35	CB	GLU- 543	4.06	0	Hydrophobic	false
C34	CG	GLU- 543	3.68	0	Hydrophobic	false
C35	CD	ARG- 547	3.91	0	Hydrophobic	false
F01	CG	PRO- 667	3.2	0	Hydrophobic	false
F03	CB	PRO- 667	3.44	0	Hydrophobic	false
F03	SG	CYS- 680	3.39	0	Hydrophobic	false
C13	CB	PHE- 738	4.18	0	Hydrophobic	false
C12	CD1	PHE- 738	3.27	0	Hydrophobic	false
S30	CD2	LEU- 810	3.86	0	Hydrophobic	false
C31	CD1	LEU- 810	4.21	0	Hydrophobic	false
F01	CB	GLU- 840	4.48	0	Hydrophobic	false
F04	CB	GLU- 840	3.91	0	Hydrophobic	false
C36	CB	HIS- 843	3.47	0	Hydrophobic	false