scPDB - 5a3b entry

Protein Data Bank Entry:

PDB ID : 5a3b

Resolution :1.900 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:	11.701
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.226	941.625

% Hydrophobic	% Polar
46.95	53.05
According to VolSite

Ligand :

HET Code:	APR
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	-
Buried Surface Area:	63.09 %
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
13.1637	19.5404	37.6696

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- 34	2.71	155.53	H-Bond (Protein Donor)	false
C1D	CD1	LEU- 66	4.24	0	Hydrophobic	false
O2D	O	THR- 117	2.66	154.34	H-Bond (Ligand Donor)	false
C3D	CB	THR- 117	3.85	0	Hydrophobic	false
O3D	NE2	GLN- 137	2.81	146.38	H-Bond (Protein Donor)	false
O1B	N	GLY- 231	2.7	171.04	H-Bond (Protein Donor)	false
O2A	N	THR- 233	3.3	151.66	H-Bond (Protein Donor)	false
C5D	CB	THR- 233	3.71	0	Hydrophobic	false
C4D	CG2	THR- 233	3.64	0	Hydrophobic	false
O3D	OG1	THR- 234	2.71	170.64	H-Bond (Ligand Donor)	false
C4D	CG2	THR- 234	4.13	0	Hydrophobic	false
O2'	OD1	ASN- 258	2.97	164.02	H-Bond (Ligand Donor)	false
O3'	ND2	ASN- 258	2.99	157.16	H-Bond (Protein Donor)	false
N3	N	HIS- 259	3.1	160.61	H-Bond (Protein Donor)	false
DuAr	DuAr	HIS- 259	3.56	0	Aromatic Face/Face	false
C3'	CZ	TYR- 262	4.49	0	Hydrophobic	false
O3'	OH	TYR- 262	2.56	151.8	H-Bond (Ligand Donor)	false
N6	ND1	HIS- 278	3.46	133.48	H-Bond (Ligand Donor)	false
N1	N	ILE- 279	3.03	171.43	H-Bond (Protein Donor)	false