scPDB - 3v3n entry

Protein Data Bank Entry:

PDB ID : 3v3n

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2011-12-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	TetX family tetracycline inactivation enzyme
ID:	Q93L51_BACT4
AC:	Q93L51
Organism:	Bacteroides thetaiotaomicron
Reign:	Bacteria
TaxID:	818
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	52.471
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.559	648.000

% Hydrophobic	% Polar
46.35	53.65
According to VolSite

Ligand :

HET Code:	MIY
Formula:	C23H25N3O7
Molecular weight:	455.460 g/mol
DrugBank ID:	DB01017
Buried Surface Area:	60.56 %
Polar Surface area:	174.32 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	3
Rings:	4
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
-53.2839	-6.68867	9.84803

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	NE2	GLN- 192	3.18	147.39	H-Bond (Protein Donor)	false
CN7	SD	MET- 215	3.93	0	Hydrophobic	false
C5	CG	PHE- 224	4.24	0	Hydrophobic	false
C6	CD2	PHE- 224	3.38	0	Hydrophobic	false
C8	CE2	PHE- 224	3.55	0	Hydrophobic	false
C71	CE	MET- 375	3.52	0	Hydrophobic	false
CN7	CE1	PHE- 382	4.02	0	Hydrophobic	false
O7	N5	FAD- 2004	2.82	126.89	H-Bond (Ligand Donor)	false