scPDB - 4dx7 entry

Protein Data Bank Entry:

PDB ID : 4dx7

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2012-02-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Multidrug efflux pump subunit AcrB
ID:	ACRB_ECOLI
AC:	P31224
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	59.618
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.356	2207.250

% Hydrophobic	% Polar
25.99	74.01
According to VolSite

Ligand :

HET Code:	DM2
Formula:	C27H28NO11
Molecular weight:	542.511 g/mol
DrugBank ID:	DB00997
Buried Surface Area:	42.6 %
Polar Surface area:	213.34 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
34.4707	-20.5762	-2.20146

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
C15	CE	MET- 575	3.72	0	Hydrophobic	false
C12	CB	PHE- 617	4.25	0	Hydrophobic	false
C14	CG	PHE- 617	3.98	0	Hydrophobic	false
C11	CB	PHE- 617	3.29	0	Hydrophobic	false
C4	CB	THR- 676	4.46	0	Hydrophobic	false
C21	CG2	THR- 676	3.4	0	Hydrophobic	false
O4	OG1	THR- 676	3.43	136.66	H-Bond (Protein Donor)	false
O12	ND2	ASN- 719	2.9	120.89	H-Bond (Protein Donor)	false
O12	OD1	ASN- 719	2.81	158.18	H-Bond (Ligand Donor)	false
N3'	OE1	GLU- 826	2.81	144.1	H-Bond (Ligand Donor)	false
N3'	OE1	GLU- 826	2.81	0	Ionic (Ligand Cationic)	false
N3'	OE2	GLU- 826	3.87	0	Ionic (Ligand Cationic)	false
C7	CG	LEU- 828	4.5	0	Hydrophobic	false
C18	CD2	LEU- 828	4.49	0	Hydrophobic	false
C19	CG	LEU- 828	4.48	0	Hydrophobic	false
C20	CB	LEU- 828	4.22	0	Hydrophobic	false
C5	CG	LEU- 828	4.15	0	Hydrophobic	false
C3	CG	GLN- 830	4.26	0	Hydrophobic	false
C21	SD	MET- 862	4.1	0	Hydrophobic	false