scPDB - 2h59 entry

Protein Data Bank Entry:

PDB ID : 2h59

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2006-05-25

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
ID:	NPD_THEMA
AC:	Q9WYW0
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.788
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.798	459.000

% Hydrophobic	% Polar
52.21	47.79
According to VolSite

Ligand :

HET Code:	APR
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	-
Buried Surface Area:	71.26 %
Polar Surface area:	316.8 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-8.51403	3.41717	0.572167

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
O2D	NZ	LYS- 11	2.76	143.23	H-Bond (Protein Donor)	false
O2B	N	ALA- 22	2.73	158.24	H-Bond (Protein Donor)	false
N6	OG1	THR- 26	3.29	145.02	H-Bond (Ligand Donor)	false
N7	OG1	THR- 26	2.83	154.94	H-Bond (Protein Donor)	false
C5'	CB	ASP- 32	4.15	0	Hydrophobic	false
O2A	N	PHE- 33	2.83	146.76	H-Bond (Protein Donor)	false
C1D	CG	PHE- 33	3.95	0	Hydrophobic	false
C4D	CD1	PHE- 33	3.95	0	Hydrophobic	false
C3D	CE1	PHE- 33	3.39	0	Hydrophobic	false
O1A	NH1	ARG- 34	2.83	159.53	H-Bond (Protein Donor)	false
O2A	N	ARG- 34	2.89	157.7	H-Bond (Protein Donor)	false
O5D	NH1	ARG- 34	3.34	123.75	H-Bond (Protein Donor)	false
O4D	NH1	ARG- 34	3.19	161.7	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 34	3.88	0	Ionic (Protein Cationic)	false
O1D	OH	TYR- 40	2.74	162.76	H-Bond (Protein Donor)	false
C1D	CE1	TYR- 40	4.14	0	Hydrophobic	false
O1B	OG	SER- 189	2.75	172.15	H-Bond (Protein Donor)	false
C3'	CB	SER- 190	4.36	0	Hydrophobic	false
O1A	OG	SER- 190	2.65	174.18	H-Bond (Protein Donor)	false
O1B	N	SER- 190	3.02	154.22	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 193	3.87	0	Hydrophobic	false
O3'	ND2	ASN- 214	3.13	164.91	H-Bond (Protein Donor)	false
N3	N	LEU- 215	3.05	169.13	H-Bond (Protein Donor)	false
C1'	CB	LEU- 215	4.49	0	Hydrophobic	false
O2'	O	LEU- 215	2.52	148.69	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 231	2.94	131.48	H-Bond (Ligand Donor)	false
N1	N	VAL- 232	2.94	151.27	H-Bond (Protein Donor)	false