scPDB - 4yvg entry

Protein Data Bank Entry:

PDB ID : 4yvg

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2015-03-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA (guanine-N(1)-)-methyltransferase
ID:	TRMD_HAEIN
AC:	P43912
Organism:	Haemophilus influenzae
Reign:	Bacteria
TaxID:	71421
EC Number:	2.1.1.228

Chains:

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

Ligand binding site composition:

B-Factor:	15.549
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.361	259.875

% Hydrophobic	% Polar
42.86	57.14
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	69.98 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
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
45.8136	4.63711	10.5984

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
O3'	OH	TYR- 86	2.73	153.47	H-Bond (Ligand Donor)	false
O2'	O	LEU- 87	2.65	159.96	H-Bond (Ligand Donor)	false
O	NE2	GLN- 90	2.81	155.4	H-Bond (Protein Donor)	false
N	OE1	GLU- 116	3.18	164.42	H-Bond (Ligand Donor)	false
N	OE1	GLU- 116	3.18	0	Ionic (Ligand Cationic)	false
N1	N	ILE- 133	3.17	165.35	H-Bond (Protein Donor)	false
N6	O	GLY- 134	3.07	128.42	H-Bond (Ligand Donor)	false
N6	O	TYR- 136	2.81	151.48	H-Bond (Ligand Donor)	false
CB	CG1	VAL- 137	4.26	0	Hydrophobic	false
SD	CG1	VAL- 137	4.08	0	Hydrophobic	false
N7	N	LEU- 138	3.05	175.24	H-Bond (Protein Donor)	false