scPDB - 5a3c entry

Protein Data Bank Entry:

PDB ID : 5a3c

Resolution :2.030 Å

Experimental Method : X-ray

Deposition Date : 2015-05-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	SIR2 family protein
ID:	Q1JGN6_STRPD
AC:	Q1JGN6
Organism:	Streptococcus pyogenes serotype M2
Reign:	Bacteria
TaxID:	370552
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.827
Number of residues:	49
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.306	931.500

% Hydrophobic	% Polar
48.91	51.09
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	68.54 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
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
13.3154	19.2155	36.4588

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
O2N	N	ALA- 34	2.67	159.37	H-Bond (Protein Donor)	false
C5D	CB	ALA- 34	4.35	0	Hydrophobic	false
C4N	CB	ALA- 34	3.72	0	Hydrophobic	false
C4N	CZ	TYR- 44	3.45	0	Hydrophobic	false
O2N	OG1	THR- 117	3.41	130.49	H-Bond (Protein Donor)	false
O2D	O	THR- 117	2.74	147.77	H-Bond (Ligand Donor)	false
C3D	CB	THR- 117	3.92	0	Hydrophobic	false
O7N	N	ALA- 119	2.81	167.4	H-Bond (Protein Donor)	false
O7N	N	ASP- 120	3.49	124.29	H-Bond (Protein Donor)	false
N7N	OD2	ASP- 120	3.31	166.33	H-Bond (Ligand Donor)	false
O3D	NE2	GLN- 137	2.97	155.77	H-Bond (Protein Donor)	false
O2D	NE2	GLN- 137	3.46	137.45	H-Bond (Protein Donor)	false
O1N	N	GLY- 231	2.93	165.63	H-Bond (Protein Donor)	false
O2A	N	THR- 233	3.22	156.29	H-Bond (Protein Donor)	false
O2A	OG1	THR- 233	2.57	171.68	H-Bond (Protein Donor)	false
C5D	CB	THR- 233	3.76	0	Hydrophobic	false
C4D	CG2	THR- 233	3.78	0	Hydrophobic	false
O3D	OG1	THR- 234	2.7	155.75	H-Bond (Protein Donor)	false
O3B	ND2	ASN- 258	3.07	143.8	H-Bond (Protein Donor)	false
O2B	OD1	ASN- 258	2.97	167.65	H-Bond (Ligand Donor)	false
N3A	N	HIS- 259	3.17	158.27	H-Bond (Protein Donor)	false
DuAr	DuAr	HIS- 259	3.55	0	Aromatic Face/Face	false
O3B	OH	TYR- 262	2.62	152.38	H-Bond (Ligand Donor)	false
N1A	N	ILE- 279	3.06	160.97	H-Bond (Protein Donor)	false
N7N	O	HOH- 2011	3.44	164.77	H-Bond (Ligand Donor)	false
O1N	O	HOH- 2123	2.64	155.55	H-Bond (Protein Donor)	false