scPDB - 4mzu entry

Protein Data Bank Entry:

PDB ID : 4mzu

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2013-09-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	WxcM-like protein
ID:	Q12KT8_SHEDO
AC:	Q12KT8
Organism:	Shewanella denitrificans
Reign:	Bacteria
TaxID:	318161
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	26 %
D	74 %

Ligand binding site composition:

B-Factor:	40.037
Number of residues:	23
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.156	651.375

% Hydrophobic	% Polar
45.60	54.40
According to VolSite

Ligand :

HET Code:	TYD
Formula:	C10H13N2O11P2
Molecular weight:	399.165 g/mol
DrugBank ID:	DB03103
Buried Surface Area:	50.83 %
Polar Surface area:	220.27 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-19.4524	-60.3914	3.81764

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
O3A	NH2	ARG- 187	3.5	133.27	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 187	3.38	0	Ionic (Protein Cationic)	false
C1'	CD2	LEU- 190	4.21	0	Hydrophobic	false
C5M	CD1	LEU- 190	4.15	0	Hydrophobic	false
C5M	CE2	PHE- 207	4.05	0	Hydrophobic	false
O2B	NE	ARG- 218	2.76	122.22	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 218	3.61	0	Ionic (Protein Cationic)	false
O2B	N	GLY- 219	3.32	162.57	H-Bond (Protein Donor)	false
O3B	N	GLY- 219	3.17	128.71	H-Bond (Protein Donor)	false
C2'	CZ	TYR- 286	3.94	0	Hydrophobic	false
C5M	CE1	TYR- 286	3.97	0	Hydrophobic	false
O2A	NH1	ARG- 293	3.28	161.97	H-Bond (Protein Donor)	false