scPDB - 4zp0 entry

Protein Data Bank Entry:

PDB ID : 4zp0

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2015-05-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Multidrug transporter MdfA
ID:	MDFA_ECOLI
AC:	P0AEY8
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:	53.280
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.379	2197.125

% Hydrophobic	% Polar
51.00	49.00
According to VolSite

Ligand :

HET Code:	DXC
Formula:	C24H39O4
Molecular weight:	391.564 g/mol
DrugBank ID:	DB03619
Buried Surface Area:	50.47 %
Polar Surface area:	80.59 Å2

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

Mass center Coordinates

X	Y	Z
-18.6716	10.4473	24.4951

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
C2	CD2	TYR- 30	3.94	0	Hydrophobic	false
C8	CE1	TYR- 30	4.08	0	Hydrophobic	false
C11	CZ	TYR- 30	4.11	0	Hydrophobic	false
C7	CB	ASN- 33	3.81	0	Hydrophobic	false
O2	OD2	ASP- 34	2.54	158.71	H-Bond (Ligand Donor)	false
C5	CE	MET- 58	4.31	0	Hydrophobic	false
C18	CE	MET- 58	3.78	0	Hydrophobic	false
C7	CE2	TYR- 61	4.47	0	Hydrophobic	false
C14	CD2	LEU- 62	4.49	0	Hydrophobic	false
C18	CD2	LEU- 62	3.51	0	Hydrophobic	false
C20	CD2	LEU- 62	3.88	0	Hydrophobic	false
C8	CG	LEU- 119	4.4	0	Hydrophobic	false
C15	CG	LEU- 119	4.04	0	Hydrophobic	false
C14	CD1	LEU- 236	4.04	0	Hydrophobic	false
C18	CD1	LEU- 236	3.86	0	Hydrophobic	false
C5	CD2	LEU- 236	3.76	0	Hydrophobic	false
C6	CD1	ILE- 239	4.16	0	Hydrophobic	false
C20	CG	MET- 358	3.48	0	Hydrophobic	false
C14	CE2	PHE- 361	4.42	0	Hydrophobic	false