scPDB - 3oii entry

Protein Data Bank Entry:

PDB ID : 3oii

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2010-08-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribosomal RNA small subunit methyltransferase NEP1
ID:	NEP1_YEAST
AC:	Q06287
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	44.817
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.154	367.875

% Hydrophobic	% Polar
33.03	66.97
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	69.98 %
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
-0.309615	0.0468077	-26.795

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
O2'	O	LEU- 180	2.83	151.14	H-Bond (Ligand Donor)	false
C2'	CB	LEU- 180	4.42	0	Hydrophobic	false
C4'	CG1	VAL- 206	4.27	0	Hydrophobic	false
C1'	CG1	VAL- 206	4.36	0	Hydrophobic	false
O2'	N	GLY- 207	3.06	162.11	H-Bond (Protein Donor)	false
N	O	GLY- 212	2.95	151.51	H-Bond (Ligand Donor)	false
OXT	N	GLY- 212	2.95	170.07	H-Bond (Protein Donor)	false
N	OD2	ASP- 214	2.97	0	Ionic (Ligand Cationic)	false
N	OD1	ASP- 214	2.97	0	Ionic (Ligand Cationic)	false
N	OD1	ASP- 214	2.97	149.24	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 214	2.55	169.03	H-Bond (Ligand Donor)	false
N1	N	LEU- 227	2.86	172.22	H-Bond (Protein Donor)	false
N6	O	SER- 228	3.19	159.14	H-Bond (Ligand Donor)	false
N6	O	TYR- 230	3.03	122.44	H-Bond (Ligand Donor)	false
N7	N	LEU- 232	2.9	146.95	H-Bond (Protein Donor)	false
C5'	CB	ALA- 234	3.95	0	Hydrophobic	false
C1'	CB	ALA- 237	3.8	0	Hydrophobic	false