scPDB - 4gi4 entry

Protein Data Bank Entry:

PDB ID : 4gi4

Resolution :1.970 Å

Experimental Method : X-ray

Deposition Date : 2012-08-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Queuine tRNA-ribosyltransferase
ID:	TGT_ZYMMO
AC:	P28720
Organism:	Zymomonas mobilis subsp. mobilis
Reign:	Bacteria
TaxID:	264203
EC Number:	2.4.2.29

Chains:

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

Ligand binding site composition:

B-Factor:	16.162
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.930	452.250

% Hydrophobic	% Polar
57.46	42.54
According to VolSite

Ligand :

HET Code:	0EX
Formula:	C26H28N7O
Molecular weight:	454.547 g/mol
DrugBank ID:	-
Buried Surface Area:	65.96 %
Polar Surface area:	124.8 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	5
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
15.3822	16.8505	18.8666

Binding mode :

What is Poseview ?

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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	CG1	VAL- 45	3.34	0	Hydrophobic	false
C14	CB	THR- 47	4.39	0	Hydrophobic	false
C15	CD2	LEU- 68	4.05	0	Hydrophobic	false
N5	OD1	ASP- 102	2.77	167.09	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 102	3.36	129.38	H-Bond (Ligand Donor)	false
N6	OD2	ASP- 102	2.64	141.52	H-Bond (Ligand Donor)	false
C6	CD2	TYR- 106	3.34	0	Hydrophobic	false
C6	CB	TYR- 106	3.58	0	Hydrophobic	false
N6	OD1	ASP- 156	2.79	152.54	H-Bond (Ligand Donor)	false
C2	SG	CYS- 158	3.54	0	Hydrophobic	false
O1	NE2	GLN- 203	2.94	155.51	H-Bond (Protein Donor)	false
O1	N	GLY- 230	2.9	146.05	H-Bond (Protein Donor)	false
N1	O	LEU- 231	2.66	156.48	H-Bond (Ligand Donor)	false
N4	O	ALA- 232	2.95	130.87	H-Bond (Ligand Donor)	false
C1	CB	ALA- 232	3.84	0	Hydrophobic	false
C5	CE	MET- 260	4	0	Hydrophobic	false
C6	CB	MET- 260	4.13	0	Hydrophobic	false
C4	CB	MET- 260	3.98	0	Hydrophobic	false
N2	OD2	ASP- 280	2.83	174.46	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 280	2.83	0	Ionic (Ligand Cationic)	false
N2	OD1	ASP- 280	3.79	0	Ionic (Ligand Cationic)	false
C14	CG1	VAL- 282	3.77	0	Hydrophobic	false