scPDB - 2nyr entry

Protein Data Bank Entry:

PDB ID : 2nyr

Resolution :2.060 Å

Experimental Method : X-ray

Deposition Date : 2006-11-21

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 deacylase sirtuin-5, mitochondrial
ID:	SIR5_HUMAN
AC:	Q9NXA8
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	55 %
B	45 %

Ligand binding site composition:

B-Factor:	18.149
Number of residues:	74
Including
Standard Amino Acids:	73
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.713	1778.625

% Hydrophobic	% Polar
48.20	51.80
According to VolSite

Ligand :

HET Code:	SVR
Formula:	C51H34N6O23S6
Molecular weight:	1291.232 g/mol
DrugBank ID:	DB04786
Buried Surface Area:	62.31 %
Polar Surface area:	551 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	6
Rings:	8
Aromatic rings:	8
Anionic atoms:	6
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
9.23687	-14.2689	10.1568

Binding mode :

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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
C70	CB	ALA- 59	4.21	0	Hydrophobic	false
C70	CG2	THR- 69	3.78	0	Hydrophobic	false
O35	N	PHE- 70	3.45	135.88	H-Bond (Protein Donor)	false
O36	N	PHE- 70	3.48	162.37	H-Bond (Protein Donor)	false
O82	N	PHE- 70	2.95	168.09	H-Bond (Protein Donor)	false
C72	CB	PHE- 70	3.64	0	Hydrophobic	false
C18	CD	ARG- 71	4.23	0	Hydrophobic	false
C62	CG	ARG- 71	3.97	0	Hydrophobic	false
C67	CB	ARG- 71	3.65	0	Hydrophobic	false
O23	CZ	ARG- 71	3.99	0	Ionic (Protein Cationic)	false
O24	CZ	ARG- 71	3.85	0	Ionic (Protein Cationic)	false
O24	NE	ARG- 71	3.28	156.18	H-Bond (Protein Donor)	false
C16	CB	ALA- 82	4.25	0	Hydrophobic	false
C12	CB	ALA- 86	3.78	0	Hydrophobic	false
O30	OH	TYR- 102	2.8	167.19	H-Bond (Protein Donor)	false
O86	OH	TYR- 102	2.96	141.07	H-Bond (Protein Donor)	false
O28	CZ	ARG- 105	3.57	0	Ionic (Protein Cationic)	false
O29	CZ	ARG- 105	3.63	0	Ionic (Protein Cationic)	false
O82	CZ	ARG- 105	3.99	0	Ionic (Protein Cationic)	false
O85	CZ	ARG- 105	3.94	0	Ionic (Protein Cationic)	false
O84	CZ	ARG- 105	3.87	0	Ionic (Protein Cationic)	false
O28	NH1	ARG- 105	2.71	165.55	H-Bond (Protein Donor)	false
O29	NH2	ARG- 105	2.9	152.46	H-Bond (Protein Donor)	false
O85	NE	ARG- 105	3.48	149.78	H-Bond (Protein Donor)	false
O85	NH2	ARG- 105	3.48	147.56	H-Bond (Protein Donor)	false
O80	ND2	ASN- 141	3.43	131.36	H-Bond (Protein Donor)	false
O32	N	GLY- 224	3.05	130.52	H-Bond (Protein Donor)	false
C42	CB	ASN- 226	3.98	0	Hydrophobic	false
C40	CD1	LEU- 227	3.89	0	Hydrophobic	false
C42	CG	LEU- 227	3.98	0	Hydrophobic	false
C38	CD1	LEU- 232	3.69	0	Hydrophobic	false
C50	CD2	LEU- 232	3.53	0	Hydrophobic	false
O25	N	TYR- 255	3.47	161.38	H-Bond (Protein Donor)	false
C27	CD2	TYR- 255	3.77	0	Hydrophobic	false
C46	CD1	TYR- 255	3.49	0	Hydrophobic	false
C14	CB	TYR- 255	3.73	0	Hydrophobic	false
C49	CB	TYR- 255	3.84	0	Hydrophobic	false
C27	CB	MET- 259	3.77	0	Hydrophobic	false
C50	CE	MET- 259	3.54	0	Hydrophobic	false
C33	CE	MET- 259	3.42	0	Hydrophobic	false