scPDB - 2od7 entry

Protein Data Bank Entry:

PDB ID : 2od7

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2006-12-21

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 %

Ligand binding site composition:

B-Factor:	25.940
Number of residues:	36
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.684	563.625

% Hydrophobic	% Polar
49.70	50.30
According to VolSite

Ligand :

HET Code:	A1R
Formula:	C15H23N6O12P2
Molecular weight:	541.324 g/mol
DrugBank ID:	-
Buried Surface Area:	58.12 %
Polar Surface area:	303.95 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
43.2412	59.0701	31.3529

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
O2B	N	ALA- 33	2.54	159.53	H-Bond (Protein Donor)	false
C5N	CB	ALA- 33	4.45	0	Hydrophobic	false
N7	OG1	THR- 37	3.38	147.96	H-Bond (Protein Donor)	false
C2N	CZ	PHE- 44	4.23	0	Hydrophobic	false
O1A	NH2	ARG- 45	2.6	176.65	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 45	3.46	161.92	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 45	3.52	0	Ionic (Protein Cationic)	false
O2N	OE1	GLU- 64	2.96	159.86	H-Bond (Ligand Donor)	false
C2N	CZ	PHE- 184	4.03	0	Hydrophobic	false
O2A	OG	SER- 225	3	170.22	H-Bond (Protein Donor)	false
O1B	N	SER- 225	3.38	159.44	H-Bond (Protein Donor)	false
C3'	CB	SER- 225	4.2	0	Hydrophobic	false
C3N	CG2	VAL- 228	3.95	0	Hydrophobic	false
O3'	ND2	ASN- 248	3.05	172.7	H-Bond (Protein Donor)	false
N1	N	SER- 270	2.69	154.19	H-Bond (Protein Donor)	false
O1B	O	HOH- 1024	2.88	179.98	H-Bond (Protein Donor)	false