scPDB - 3lcu entry

Protein Data Bank Entry:

PDB ID : 3lcu

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2010-01-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	16S rRNA (guanine(1405)-N(7))-methyltransferase
ID:	SGM_MICZI
AC:	Q7M0R2
Organism:	Micromonospora zionensis
Reign:	Bacteria
TaxID:	1879
EC Number:	2.1.1.179

Chains:

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

Ligand binding site composition:

B-Factor:	15.958
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.539	249.750

% Hydrophobic	% Polar
56.76	43.24
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	82.27 %
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
8.69885	1.61119	19.0812

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
SD	CZ	PHE- 64	3.88	0	Hydrophobic	false
C5'	CE2	PHE- 64	3.87	0	Hydrophobic	false
C3'	CD2	PHE- 64	4.05	0	Hydrophobic	false
O3'	NE2	HIS- 102	3.11	153.17	H-Bond (Protein Donor)	false
SD	CB	SER- 104	3.41	0	Hydrophobic	false
CG	CB	SER- 104	3.77	0	Hydrophobic	false
OXT	OG1	THR- 105	3.09	165.01	H-Bond (Protein Donor)	false
O	NH1	ARG- 108	2.8	148.03	H-Bond (Protein Donor)	false
O	NH2	ARG- 108	2.92	141.4	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 108	2.73	140.04	H-Bond (Protein Donor)	false
O	CZ	ARG- 108	3.28	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 108	3.58	0	Ionic (Protein Cationic)	false
N	O	ALA- 133	2.73	166.86	H-Bond (Ligand Donor)	false
C4'	CB	ALA- 133	3.97	0	Hydrophobic	false
C1'	CB	ALA- 133	3.77	0	Hydrophobic	false
O3'	OD2	ASP- 156	2.75	140.33	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 156	2.7	160.97	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 182	2.88	154.46	H-Bond (Ligand Donor)	false
N1	N	LEU- 183	2.91	165.4	H-Bond (Protein Donor)	false
N	O	LEU- 198	2.86	149.44	H-Bond (Ligand Donor)	false
CG	CB	LYS- 199	4.35	0	Hydrophobic	false
N7	NE2	GLN- 207	2.83	164.33	H-Bond (Protein Donor)	false
N6	OE1	GLN- 207	3.28	163.44	H-Bond (Ligand Donor)	false
N	O	HOH- 277	3.32	128.91	H-Bond (Ligand Donor)	false
N	O	HOH- 280	2.97	138.87	H-Bond (Ligand Donor)	false