scPDB - 3bbh entry

Protein Data Bank Entry:

PDB ID : 3bbh

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2007-11-09

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_METJA
AC:	Q57977
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	2.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	53.626
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.515	482.625

% Hydrophobic	% Polar
41.26	58.74
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	74.84 %
Polar Surface area:	214.71 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
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
25.5999	63.4627	27.3529

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
O	OG1	THR- 142	3.4	147.73	H-Bond (Protein Donor)	false
OXT	N	LYS- 143	2.81	162.61	H-Bond (Protein Donor)	false
C4'	CG2	ILE- 161	4.07	0	Hydrophobic	false
C1'	CG2	ILE- 161	4.11	0	Hydrophobic	false
O3'	N	GLY- 162	3.3	125.77	H-Bond (Protein Donor)	false
O2'	N	GLY- 162	3.15	173.49	H-Bond (Protein Donor)	false
CG	CE1	PHE- 164	4.15	0	Hydrophobic	false
NE	O	PHE- 164	3.19	143.27	H-Bond (Ligand Donor)	false
NE	O	PRO- 165	3.08	122.9	H-Bond (Ligand Donor)	false
N1	N	ILE- 185	3.12	159.79	H-Bond (Protein Donor)	false
N6	O	TYR- 186	2.79	156.25	H-Bond (Ligand Donor)	false
N7	N	LEU- 190	2.8	176.87	H-Bond (Protein Donor)	false
C5'	CB	ALA- 192	4.09	0	Hydrophobic	false
C1'	CG2	VAL- 195	3.77	0	Hydrophobic	false