scPDB - 4cby entry

Protein Data Bank Entry:

PDB ID : 4cby

Resolution :2.720 Å

Experimental Method : X-ray

Deposition Date : 2013-10-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Histone deacetylase 4
ID:	HDAC4_HUMAN
AC:	P56524
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:	29.566
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.936	405.000

% Hydrophobic	% Polar
65.83	34.17
According to VolSite

Ligand :

HET Code:	KEE
Formula:	C19H16N2O3
Molecular weight:	320.342 g/mol
DrugBank ID:	-
Buried Surface Area:	52.3 %
Polar Surface area:	75.36 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
29.0626	-14.4899	11.1689

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
C15	CB	PRO- 676	3.82	0	Hydrophobic	false
C13	CB	GLU- 677	3.71	0	Hydrophobic	false
C14	CD	ARG- 681	4.16	0	Hydrophobic	false
O24	NE2	HIS- 802	2.61	161.45	H-Bond (Protein Donor)	false
N23	NE2	HIS- 803	3.07	126.25	H-Bond (Ligand Donor)	false
C4	CD2	PHE- 812	3.64	0	Hydrophobic	false
DuAr	DuAr	PHE- 871	3.99	0	Aromatic Face/Face	false
C7	CB	PHE- 871	3.76	0	Hydrophobic	false
C15	CB	HIS- 976	4.2	0	Hydrophobic	false
O22	ZN	ZN- 2034	2.01	0	Metal Acceptor	false
O24	ZN	ZN- 2034	2.16	0	Metal Acceptor	false