scPDB - 3tfj entry

Protein Data Bank Entry:

PDB ID : 3tfj

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2011-08-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dimethylsulfonioproprionate demethylase DmdA
ID:	DMDA_PELUB
AC:	Q4FP21
Organism:	Pelagibacter ubique
Reign:	Bacteria
TaxID:	335992
EC Number:	2.1.1.269

Chains:

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

Ligand binding site composition:

B-Factor:	24.801
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.196	1113.750

% Hydrophobic	% Polar
43.33	56.67
According to VolSite

Ligand :

HET Code:	THG
Formula:	C19H21N7O6
Molecular weight:	443.413 g/mol
DrugBank ID:	DB02031
Buried Surface Area:	60.86 %
Polar Surface area:	212.92 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	6
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
11.9024	7.55809	16.8433

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
C7	CG	GLU- 63	4.4	0	Hydrophobic	false
CB	CB	TYR- 95	4.34	0	Hydrophobic	false
C6'	CG2	VAL- 110	3.43	0	Hydrophobic	false
N1	OG	SER- 122	2.84	154.11	H-Bond (Protein Donor)	false
N8	O	SER- 122	2.84	163.26	H-Bond (Ligand Donor)	false
N2	OG	SER- 122	3.02	137.37	H-Bond (Ligand Donor)	false
C7	CB	ALA- 124	3.97	0	Hydrophobic	false
CG	CE2	PHE- 177	3.82	0	Hydrophobic	false
CG	CZ	PHE- 178	4.05	0	Hydrophobic	false
N3	OE1	GLU- 204	2.83	134.66	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 204	2.83	138.4	H-Bond (Ligand Donor)	false
C2'	CD2	LEU- 244	3.94	0	Hydrophobic	false
OE2	OH	TYR- 265	2.58	146.61	H-Bond (Protein Donor)	false
OE2	O	HOH- 670	3.26	123.5	H-Bond (Protein Donor)	false