scPDB - 1szc entry

Protein Data Bank Entry:

PDB ID : 1szc

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2004-04-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD-dependent protein deacetylase HST2
ID:	HST2_YEAST
AC:	P53686
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	3.5.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %
B	0 %

Ligand binding site composition:

B-Factor:	28.474
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.703	513.000

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	CNA
Formula:	C22H28N7O13P2
Molecular weight:	660.444 g/mol
DrugBank ID:	DB02498
Buried Surface Area:	60.94 %
Polar Surface area:	334.31 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-9.99489	34.2046	-42.2308

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
O3D	OH	ALY- 16	3.21	134.61	H-Bond (Ligand Donor)	false
O2D	OH	ALY- 16	2.76	163.39	H-Bond (Ligand Donor)	false
O2N	N	ALA- 33	2.87	157.01	H-Bond (Protein Donor)	false
C3N	CB	ALA- 33	3.8	0	Hydrophobic	false
N6A	OG1	THR- 37	3.33	138.24	H-Bond (Ligand Donor)	false
C4N	CG2	ILE- 41	4.4	0	Hydrophobic	false
C2D	CE2	PHE- 44	4.42	0	Hydrophobic	false
O1A	CZ	ARG- 45	3.6	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 45	2.69	169.99	H-Bond (Protein Donor)	false
C5D	CB	GLN- 115	4.5	0	Hydrophobic	false
O7N	N	ILE- 117	2.89	163.39	H-Bond (Protein Donor)	false
N7N	OD1	ASP- 118	2.89	164.84	H-Bond (Ligand Donor)	false
O1N	OG1	THR- 224	3.09	162.85	H-Bond (Protein Donor)	false
O2A	OG	SER- 225	2.78	177.96	H-Bond (Protein Donor)	false
O1N	N	SER- 225	2.92	162.04	H-Bond (Protein Donor)	false
C3B	CB	SER- 225	4.28	0	Hydrophobic	false
C5D	CG2	VAL- 228	4.08	0	Hydrophobic	false
C3D	CG2	VAL- 228	4.41	0	Hydrophobic	false
O3B	ND2	ASN- 248	3.37	172.79	H-Bond (Protein Donor)	false
C1B	CG	LEU- 249	4.43	0	Hydrophobic	false
N1A	N	SER- 270	2.74	148.16	H-Bond (Protein Donor)	false