scPDB - 3axs entry

Protein Data Bank Entry:

PDB ID : 3axs

Resolution :2.160 Å

Experimental Method : X-ray

Deposition Date : 2011-04-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase
ID:	TRM1_AQUAE
AC:	O67010
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	37.038
Number of residues:	34
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.247	344.250

% Hydrophobic	% Polar
51.96	48.04
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	63.93 %
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
24.0813	12.727	45.7712

Binding mode :

What is Poseview ?

2D View
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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
OXT	NH2	ARG- 36	3.12	149.62	H-Bond (Protein Donor)	false
N	O	LEU- 60	3.02	160.61	H-Bond (Ligand Donor)	false
CG	CB	LEU- 60	4.4	0	Hydrophobic	false
C1'	CD2	LEU- 60	4.11	0	Hydrophobic	false
C4'	CB	LEU- 60	4	0	Hydrophobic	false
CG	CB	ALA- 62	3.77	0	Hydrophobic	false
OXT	NE	ARG- 66	3.05	146.84	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 66	3.88	0	Ionic (Protein Cationic)	false
O3'	OD2	ASP- 84	2.66	165.48	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 84	3.41	127.41	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 84	2.59	152.2	H-Bond (Ligand Donor)	false
N3	N	ILE- 85	3.31	157.85	H-Bond (Protein Donor)	false
N6	OE2	GLU- 113	3.21	152.97	H-Bond (Ligand Donor)	false
N1	N	ALA- 114	2.89	139.25	H-Bond (Protein Donor)	false
N	OD1	ASP- 132	2.72	154.61	H-Bond (Ligand Donor)	false
NE	O	ASP- 132	3.1	164.78	H-Bond (Ligand Donor)	false
N	OD1	ASP- 132	2.72	0	Ionic (Ligand Cationic)	false
C5'	CE2	PHE- 134	4	0	Hydrophobic	false
C3'	CE2	PHE- 134	4.21	0	Hydrophobic	false
O	O	HOH- 395	2.53	179.94	H-Bond (Protein Donor)	false
N	O	HOH- 396	3.27	147.4	H-Bond (Ligand Donor)	false
O	O	HOH- 399	2.8	179.99	H-Bond (Protein Donor)	false