scPDB - 1i9g entry

Protein Data Bank Entry:

PDB ID : 1i9g

Resolution :1.980 Å

Experimental Method : X-ray

Deposition Date : 2001-03-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA (adenine(58)-N(1))-methyltransferase TrmI
ID:	TRMI_MYCTU
AC:	P9WFZ1
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.114
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.428	627.750

% Hydrophobic	% Polar
40.86	59.14
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	70.16 %
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
15.1708	-10.4144	19.2858

Binding mode :

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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
SD	CB	PRO- 80	4.18	0	Hydrophobic	false
O	N	ILE- 83	3.04	158.86	H-Bond (Protein Donor)	false
OXT	N	SER- 110	2.98	135.65	H-Bond (Protein Donor)	false
OXT	N	ALA- 112	3.38	153.98	H-Bond (Protein Donor)	false
O	N	LEU- 113	3.17	151.89	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 131	3.14	124.49	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 131	2.64	169.39	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 131	2.58	163.06	H-Bond (Ligand Donor)	false
N3	N	GLN- 132	3.1	160.01	H-Bond (Protein Donor)	false
O3'	ND1	HIS- 136	2.62	166.09	H-Bond (Protein Donor)	false
O2'	ND1	HIS- 136	3.41	122.57	H-Bond (Protein Donor)	false
N6	OD2	ASP- 161	3.03	144.37	H-Bond (Ligand Donor)	false
N1	N	LEU- 162	3.03	165.95	H-Bond (Protein Donor)	false
N	OD1	ASP- 178	2.64	170.83	H-Bond (Ligand Donor)	false
N	OD1	ASP- 178	2.64	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 178	4.34	0	Hydrophobic	false
N	O	HOH- 386	2.75	166.41	H-Bond (Ligand Donor)	false