scPDB - 5fkk entry

Protein Data Bank Entry:

PDB ID : 5fkk

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2015-10-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tetracycline repressor protein class D
ID:	TETR4_ECOLX
AC:	P0ACT4
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	15 %
B	85 %

Ligand binding site composition:

B-Factor:	28.907
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.320	374.625

% Hydrophobic	% Polar
54.05	45.95
According to VolSite

Ligand :

HET Code:	TDC
Formula:	C22H21N2O7
Molecular weight:	425.411 g/mol
DrugBank ID:	-
Buried Surface Area:	64.95 %
Polar Surface area:	168.24 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
3.45416	15.5003	54.4943

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
O3	NE2	HIS- 64	2.62	166	H-Bond (Protein Donor)	false
C9	CD	ARG- 104	3.83	0	Hydrophobic	false
C6	CG	PRO- 105	4.38	0	Hydrophobic	false
C1A	CG	PRO- 105	3.61	0	Hydrophobic	false
C1A	CG	PRO- 105	3.61	0	Hydrophobic	false
C62	CB	VAL- 113	4.35	0	Hydrophobic	false
C5	CG2	VAL- 113	4.19	0	Hydrophobic	false
C6	CG1	VAL- 113	3.64	0	Hydrophobic	false
O3	NE2	GLN- 116	2.95	166.2	H-Bond (Protein Donor)	false
C62	CG	LEU- 117	4.3	0	Hydrophobic	false
C7	CD1	LEU- 131	3.87	0	Hydrophobic	false
C5	CG2	ILE- 134	3.76	0	Hydrophobic	false
C62	CG2	ILE- 134	3.76	0	Hydrophobic	false
C7	CD1	LEU- 170	4.08	0	Hydrophobic	false
C9	CD2	LEU- 174	3.68	0	Hydrophobic	false
C7	SD	MET- 177	4.32	0	Hydrophobic	false
C9	CE	MET- 177	3.35	0	Hydrophobic	false
O12	MG	MG- 223	2	0	Metal Acceptor	false
O11	MG	MG- 223	1.89	0	Metal Acceptor	false