scPDB - 4zu4 entry

Protein Data Bank Entry:

PDB ID : 4zu4

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2015-05-15

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
A	79 %
B	21 %

Ligand binding site composition:

B-Factor:	24.026
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.565	506.250

% Hydrophobic	% Polar
45.33	54.67
According to VolSite

Ligand :

HET Code:	4TG
Formula:	C17H25N3O15P2
Molecular weight:	573.339 g/mol
DrugBank ID:	-
Buried Surface Area:	65.39 %
Polar Surface area:	285.22 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-4.26078	-21.7174	-40.2849

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
C4'	CG1	VAL- 183	3.84	0	Hydrophobic	false
C1'	CG2	VAL- 183	4.15	0	Hydrophobic	false
O1B	NH1	ARG- 187	2.96	153.76	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 187	2.7	143.45	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 187	3.89	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 187	3.53	0	Ionic (Protein Cationic)	false
C5'	CD1	LEU- 190	4.18	0	Hydrophobic	false
C5M	CD1	LEU- 190	4.03	0	Hydrophobic	false
C1Q	CD1	LEU- 190	3.96	0	Hydrophobic	false
O4	NH2	ARG- 205	2.69	140.23	H-Bond (Protein Donor)	false
C1Q	CE2	PHE- 207	3.93	0	Hydrophobic	false
C5M	CE1	PHE- 207	3.75	0	Hydrophobic	false
C5Q	CE2	PHE- 207	4.38	0	Hydrophobic	false
C2Q	CZ	PHE- 207	3.79	0	Hydrophobic	false
O2B	NE	ARG- 218	2.83	159.74	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 218	3.13	138.75	H-Bond (Protein Donor)	false
O3A	NH1	ARG- 218	3.31	134.69	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 218	3.41	0	Ionic (Protein Cationic)	false
O1B	N	GLY- 219	2.87	161.08	H-Bond (Protein Donor)	false
O	ND1	HIS- 221	2.89	157.41	H-Bond (Protein Donor)	false
O3Q	NE2	HIS- 223	2.73	152.87	H-Bond (Ligand Donor)	false
N4Q	OE1	GLN- 228	2.9	151.01	H-Bond (Ligand Donor)	false
O3Q	NE2	GLN- 228	3.1	171.31	H-Bond (Protein Donor)	false
C6Q	CG	GLN- 269	4.02	0	Hydrophobic	false
O	NE2	GLN- 269	3.46	152.11	H-Bond (Protein Donor)	false
C6Q	CD2	LEU- 278	4.44	0	Hydrophobic	false
C6Q	CG2	VAL- 280	4.41	0	Hydrophobic	false
C2'	CZ	TYR- 286	4.15	0	Hydrophobic	false
C5M	CD1	TYR- 286	4.18	0	Hydrophobic	false
O2Q	OH	TYR- 291	2.69	171.99	H-Bond (Protein Donor)	false
C3Q	CE2	TYR- 291	4.02	0	Hydrophobic	false
O3Q	O	HOH- 575	3.12	179.97	H-Bond (Protein Donor)	false