scPDB - 3c10 entry

Protein Data Bank Entry:

PDB ID : 3c10

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2008-01-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.520	6.650	6.710	0.090	6.710	3

List of CHEMBLId :

CHEMBL99

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
C	100 %

Ligand binding site composition:

B-Factor:	39.132
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.476	317.250

% Hydrophobic	% Polar
60.64	39.36
According to VolSite

Ligand :

HET Code:	TSN
Formula:	C17H22N2O3
Molecular weight:	302.368 g/mol
DrugBank ID:	DB04297
Buried Surface Area:	52.2 %
Polar Surface area:	69.64 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
7.80036	52.864	-14.725

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
O1	ZN	ZN- 101	1.99	0	Metal Acceptor	false
O2	ZN	ZN- 101	2.66	0	Metal Acceptor	false
C17	CG	PRO- 542	4.24	0	Hydrophobic	false
C4	CG	PRO- 542	4.04	0	Hydrophobic	false
C15	CB	ASP- 626	4.14	0	Hydrophobic	false
O1	NE2	HIS- 669	2.55	175.01	H-Bond (Protein Donor)	false
O1	NE2	HIS- 670	3.03	132.33	H-Bond (Protein Donor)	false
C15	CE2	PHE- 679	3.63	0	Hydrophobic	false
C14	CD2	PHE- 738	3.51	0	Hydrophobic	false
C15	CE1	PHE- 738	3.99	0	Hydrophobic	false
C2	CG	LEU- 810	3.46	0	Hydrophobic	false
C3	CD1	LEU- 810	3.67	0	Hydrophobic	false