scPDB - 5d7p entry

Protein Data Bank Entry:

PDB ID : 5d7p

Resolution :1.760 Å

Experimental Method : X-ray

Deposition Date : 2015-08-14

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 sirtuin-2
ID:	SIR2_HUMAN
AC:	Q8IXJ6
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.5.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
B	98 %

Ligand binding site composition:

B-Factor:	27.189
Number of residues:	45
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.510	1198.125

% Hydrophobic	% Polar
59.44	40.56
According to VolSite

Ligand :

HET Code:	AR6
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	DB02059
Buried Surface Area:	77.5 %
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
14.2145	-16.1665	-57.2323

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
O2B	N	ALA- 85	2.81	161.54	H-Bond (Protein Donor)	false
N6	OG1	THR- 89	3.09	148.16	H-Bond (Ligand Donor)	false
N7	OG1	THR- 89	2.81	160.5	H-Bond (Protein Donor)	false
C5'	CB	ASP- 95	3.98	0	Hydrophobic	false
O2A	N	PHE- 96	2.69	148.91	H-Bond (Protein Donor)	false
C3D	CE2	PHE- 96	3.5	0	Hydrophobic	false
C2D	CZ	PHE- 96	3.57	0	Hydrophobic	false
O1A	NH1	ARG- 97	2.9	163.23	H-Bond (Protein Donor)	false
O1D	NH2	ARG- 97	3.45	146.66	H-Bond (Protein Donor)	false
O2A	N	ARG- 97	2.94	154.96	H-Bond (Protein Donor)	false
O4D	NH1	ARG- 97	2.89	159.44	H-Bond (Protein Donor)	false
O4D	NH2	ARG- 97	3.24	139.03	H-Bond (Protein Donor)	false
O5D	NH1	ARG- 97	3.11	123.84	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 97	3.87	0	Ionic (Protein Cationic)	false
C1D	CE2	TYR- 104	4.47	0	Hydrophobic	false
O1D	OH	TYR- 104	2.87	148.75	H-Bond (Protein Donor)	false
C5D	CB	GLN- 167	4.5	0	Hydrophobic	false
O3D	ND1	HIS- 187	2.84	156.5	H-Bond (Protein Donor)	false
O1B	OG1	THR- 262	2.68	164.25	H-Bond (Protein Donor)	false
O1B	N	SER- 263	3.19	150.81	H-Bond (Protein Donor)	false
O5'	N	SER- 263	3.29	124.07	H-Bond (Protein Donor)	false
O5'	OG	SER- 263	3.4	127.58	H-Bond (Protein Donor)	false
C3'	CB	SER- 263	4.27	0	Hydrophobic	false
C4D	CG2	VAL- 266	3.83	0	Hydrophobic	false
O3'	ND2	ASN- 286	3.04	169.07	H-Bond (Protein Donor)	false
N3	N	LYS- 287	2.96	137.24	H-Bond (Protein Donor)	false
C1'	CB	LYS- 287	4.45	0	Hydrophobic	false
O3'	OE2	GLU- 288	2.82	160.28	H-Bond (Ligand Donor)	false
N6	OE1	GLU- 323	3.04	129.74	H-Bond (Ligand Donor)	false
N1	N	CYS- 324	2.95	153.91	H-Bond (Protein Donor)	false