scPDB - 2vpr entry

Protein Data Bank Entry:

PDB ID : 2vpr

Resolution :2.490 Å

Experimental Method : X-ray

Deposition Date : 2008-03-03

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 H
ID:	TETR8_PASMD
AC:	P51561
Organism:	Pasteurella multocida
Reign:	Bacteria
TaxID:	747
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.884
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.007	695.250

% Hydrophobic	% Polar
48.06	51.94
According to VolSite

Ligand :

HET Code:	TDC
Formula:	C22H21N2O7
Molecular weight:	425.411 g/mol
DrugBank ID:	-
Buried Surface Area:	60.24 %
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
5.976	41.4513	33.4132

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	2.89	175.28	H-Bond (Protein Donor)	false
N4	OD1	ASN- 82	2.6	141.73	H-Bond (Ligand Donor)	false
O3	ND2	ASN- 82	2.74	173.53	H-Bond (Protein Donor)	false
C1C	CE1	PHE- 86	4.4	0	Hydrophobic	false
O10	NH1	ARG- 104	3.2	122.29	H-Bond (Protein Donor)	false
C9	CD	ARG- 104	3.93	0	Hydrophobic	false
O3	NE2	GLN- 116	2.79	144	H-Bond (Protein Donor)	false
O21	NE2	GLN- 116	3.07	142.79	H-Bond (Protein Donor)	false
C5	CB	LEU- 134	4.33	0	Hydrophobic	false
C62	CB	LEU- 134	3.55	0	Hydrophobic	false
C41	CB	ALA- 138	4.36	0	Hydrophobic	false
O12	MG	MG- 1207	2.04	0	Metal Acceptor	false
O11	MG	MG- 1207	2.12	0	Metal Acceptor	false