scPDB - 1qaq entry

Protein Data Bank Entry:

PDB ID : 1qaq

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 1999-03-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	rRNA adenine N-6-methyltransferase
ID:	ERM_BACIU
AC:	P13956
Organism:	Bacillus subtilis
Reign:	Bacteria
TaxID:	1423
EC Number:	2.1.1.184

Chains:

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

Ligand binding site composition:

B-Factor:	33.016
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.885	401.625

% Hydrophobic	% Polar
55.46	44.54
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	71.44 %
Polar Surface area:	214.71 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
17.2584	35.2061	24.6898

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
C2'	CG	GLN- 10	3.9	0	Hydrophobic	false
NE	OD1	ASN- 11	2.93	138.63	H-Bond (Ligand Donor)	false
NE	O	ASN- 11	3.14	137.27	H-Bond (Ligand Donor)	false
CB	CD1	PHE- 12	3.83	0	Hydrophobic	false
O	N	ILE- 13	3.02	172.97	H-Bond (Protein Donor)	false
N	OE2	GLU- 36	3.44	0	Ionic (Ligand Cationic)	false
N	O	GLY- 38	2.96	171.9	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 59	3.44	125.29	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 59	2.65	152.91	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 59	3.48	132.98	H-Bond (Ligand Donor)	false
C1'	CG2	ILE- 60	4.44	0	Hydrophobic	false
N3	N	ILE- 60	3.34	148.62	H-Bond (Protein Donor)	false
C3'	CD1	LEU- 64	4.25	0	Hydrophobic	false
N6	OD1	ASP- 84	3.39	162.95	H-Bond (Ligand Donor)	false
N1	N	ILE- 85	2.98	159.34	H-Bond (Protein Donor)	false
OXT	ND2	ASN- 101	2.55	129.62	H-Bond (Protein Donor)	false
CG	CB	ASN- 101	4.06	0	Hydrophobic	false
NE	O	ASN- 101	2.89	141.33	H-Bond (Ligand Donor)	false
C5'	CG	PRO- 103	3.77	0	Hydrophobic	false