scPDB - 3t0i entry

Protein Data Bank Entry:

PDB ID : 3t0i

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2011-07-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative methyltransferase
ID:	Q8A3I2_BACTN
AC:	Q8A3I2
Organism:	Bacteroides thetaiotaomicron
Reign:	Bacteria
TaxID:	226186
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.707
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.774	789.750

% Hydrophobic	% Polar
43.59	56.41
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	69.32 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
3.41842	-15.3914	-7.7135

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
O	NH2	ARG- 25	3.03	169.63	H-Bond (Protein Donor)	false
OXT	NE	ARG- 25	2.94	175.44	H-Bond (Protein Donor)	false
O	CZ	ARG- 25	3.82	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 25	3.8	0	Ionic (Protein Cationic)	false
SD	CB	GLN- 26	3.92	0	Hydrophobic	false
CB	CB	GLN- 26	3.62	0	Hydrophobic	false
OXT	N	GLN- 26	2.98	147.42	H-Bond (Protein Donor)	false
N	O	GLY- 54	2.71	162.25	H-Bond (Ligand Donor)	false
N	OE1	GLN- 60	3.48	123.13	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 76	2.51	163.31	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 76	3.22	147.95	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 76	3.11	154.1	H-Bond (Ligand Donor)	false
N3	N	LEU- 77	3.24	130.46	H-Bond (Protein Donor)	false
C3'	CE2	PHE- 81	4.38	0	Hydrophobic	false
N1	N	MET- 105	2.77	124.85	H-Bond (Protein Donor)	false
N	O	GLU- 121	2.88	151.29	H-Bond (Ligand Donor)	false
C5'	CB	ALA- 123	3.89	0	Hydrophobic	false
C5'	CE2	TYR- 125	4.35	0	Hydrophobic	false