scPDB - 3frk entry

Protein Data Bank Entry:

PDB ID : 3frk

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2009-01-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	QdtB
ID:	Q6TFC4_THETR
AC:	Q6TFC4
Organism:	Thermoanaerobacterium thermosaccharolyticum
Reign:	Bacteria
TaxID:	1517
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	22 %
B	78 %

Ligand binding site composition:

B-Factor:	43.710
Number of residues:	52
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.933	1130.625

% Hydrophobic	% Polar
50.15	49.85
According to VolSite

Ligand :

HET Code:	TQP
Formula:	C24H31N4O19P3
Molecular weight:	772.440 g/mol
DrugBank ID:	-
Buried Surface Area:	68.69 %
Polar Surface area:	383.84 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	4
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
34.7894	-7.47598	-14.2428

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
C1'	CB	ALA- 6	4.16	0	Hydrophobic	false
C4H	CB	ALA- 6	3.96	0	Hydrophobic	false
C1'	CE1	PHE- 8	3.98	0	Hydrophobic	false
N3	O	ASN- 30	2.88	165.03	H-Bond (Ligand Donor)	false
C2H	CZ3	TRP- 31	3.9	0	Hydrophobic	false
O4	N	PHE- 32	2.66	173.61	H-Bond (Protein Donor)	false
C5M	CG1	ILE- 33	3.61	0	Hydrophobic	false
O1P	N	GLY- 60	2.79	162.96	H-Bond (Protein Donor)	false
O2P	N	LEU- 61	3.15	138.27	H-Bond (Protein Donor)	false
C5'	CB	LEU- 61	4.29	0	Hydrophobic	false
C5'	CE2	PHE- 86	4.03	0	Hydrophobic	false
C2'	CB	PHE- 86	3.86	0	Hydrophobic	false
C5Q	CZ	PHE- 86	4.41	0	Hydrophobic	false
C4Q	CE2	PHE- 86	3.7	0	Hydrophobic	false
C2Q	CE1	PHE- 86	3.87	0	Hydrophobic	false
C5'	CB	ALA- 88	3.6	0	Hydrophobic	false
C2'	CG1	VAL- 131	3.86	0	Hydrophobic	false
N1P	OD2	ASP- 157	2.66	154.81	H-Bond (Protein Donor)	false
C2'	CB	ALA- 159	4.43	0	Hydrophobic	false
O3'	NE2	GLN- 160	2.93	173.6	H-Bond (Protein Donor)	false
C2'	CG	GLN- 160	4.42	0	Hydrophobic	false
O1P	OG	SER- 181	2.78	165.83	H-Bond (Protein Donor)	false
C5M	CZ	TYR- 183	3.58	0	Hydrophobic	false
C5Q	CE2	TYR- 183	3.95	0	Hydrophobic	false
C6Q	CZ	TYR- 183	3.58	0	Hydrophobic	false
O1A	OH	TYR- 183	2.69	154.54	H-Bond (Protein Donor)	false
C5M	CG	PRO- 184	4.25	0	Hydrophobic	false
C5H	CB	ALA- 185	3.59	0	Hydrophobic	false
O3P	OH	TYR- 214	2.82	149.32	H-Bond (Protein Donor)	false
C6Q	CZ	TYR- 214	3.63	0	Hydrophobic	false
O2A	NZ	LYS- 219	2.98	157.2	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 219	2.86	124.35	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 219	2.98	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 219	2.86	0	Ionic (Protein Cationic)	false
O2P	ND2	ASN- 228	2.87	144.5	H-Bond (Protein Donor)	false
O2Q	OH	TYR- 283	3.28	143.44	H-Bond (Protein Donor)	false
C5H	CD1	LEU- 307	4.27	0	Hydrophobic	false
O2B	NE2	HIS- 309	3.03	155.35	H-Bond (Protein Donor)	false
C2Q	CE2	TYR- 310	3.72	0	Hydrophobic	false
O1P	O	HOH- 380	2.97	179.97	H-Bond (Protein Donor)	false
O1B	O	HOH- 404	2.6	127.66	H-Bond (Protein Donor)	false