scPDB - 2xpv entry

Protein Data Bank Entry:

PDB ID : 2xpv

Resolution :1.490 Å

Experimental Method : X-ray

Deposition Date : 2010-08-30

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	100 %

Ligand binding site composition:

B-Factor:	18.640
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.832	745.875

% Hydrophobic	% Polar
45.70	54.30
According to VolSite

Ligand :

HET Code:	MIY
Formula:	C23H25N3O7
Molecular weight:	455.460 g/mol
DrugBank ID:	DB01017
Buried Surface Area:	58.55 %
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
21.1938	36.8825	34.1662

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	HIS- 64	2.81	130.27	H-Bond (Ligand Donor)	false
O8	OG	SER- 67	2.61	165.56	H-Bond (Protein Donor)	false
O2	ND2	ASN- 82	2.84	157.94	H-Bond (Protein Donor)	false
N1	OD1	ASN- 82	2.71	144.14	H-Bond (Ligand Donor)	false
C13	CD	ARG- 104	3.47	0	Hydrophobic	false
C11	CD	ARG- 104	4.27	0	Hydrophobic	false
C9	CG	PRO- 105	3.44	0	Hydrophobic	false
C6	CG2	VAL- 113	4.37	0	Hydrophobic	false
C8	CG1	VAL- 113	3.94	0	Hydrophobic	false
CN7	CG1	VAL- 113	4.45	0	Hydrophobic	false
C71	CG1	VAL- 113	4.06	0	Hydrophobic	false
O8	NE2	GLN- 116	3.41	135.76	H-Bond (Protein Donor)	false
O2	NE2	GLN- 116	3.16	147.87	H-Bond (Protein Donor)	false
CN7	CD2	LEU- 117	4.43	0	Hydrophobic	false
C71	CD1	LEU- 117	4.36	0	Hydrophobic	false
CN7	CD1	LEU- 131	3.55	0	Hydrophobic	false
C6	CG2	ILE- 134	4.03	0	Hydrophobic	false
O6	MG	MG- 1210	1.92	0	Metal Acceptor	false
O5	MG	MG- 1210	2.03	0	Metal Acceptor	false