scPDB - 1y5x entry

Protein Data Bank Entry:

PDB ID : 1y5x

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2004-12-03

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:	35.861
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.477	455.625

% Hydrophobic	% Polar
49.63	50.37
According to VolSite

Ligand :

HET Code:	E89
Formula:	C18H17N5O2
Molecular weight:	335.360 g/mol
DrugBank ID:	DB07704
Buried Surface Area:	73.08 %
Polar Surface area:	105.39 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
17.8013	-7.02912	16.9692

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
C23	CG1	VAL- 45	3.83	0	Hydrophobic	false
C19	CG1	VAL- 45	3.66	0	Hydrophobic	false
C23	CG2	THR- 47	3.83	0	Hydrophobic	false
C17	CD2	LEU- 68	3.58	0	Hydrophobic	false
C18	CD2	LEU- 68	3.47	0	Hydrophobic	false
C23	CB	ASN- 70	3.58	0	Hydrophobic	false
N25	OD1	ASP- 102	3.23	134.45	H-Bond (Ligand Donor)	false
N25	OD2	ASP- 102	2.75	135.83	H-Bond (Ligand Donor)	false
N10	OD1	ASP- 102	2.83	161.89	H-Bond (Ligand Donor)	false
C17	CB	ASP- 102	3.46	0	Hydrophobic	false
C14	CD2	TYR- 106	3.48	0	Hydrophobic	false
C4	CB	TYR- 106	3.77	0	Hydrophobic	false
DuAr	DuAr	TYR- 106	3.95	0	Aromatic Face/Face	false
N25	OD1	ASP- 156	2.89	153.24	H-Bond (Ligand Donor)	false
C2	SG	CYS- 158	3.73	0	Hydrophobic	false
O24	NE2	GLN- 203	3.17	153.27	H-Bond (Protein Donor)	false
O24	N	GLY- 230	2.92	146.74	H-Bond (Protein Donor)	false
N11	O	LEU- 231	2.85	155.35	H-Bond (Ligand Donor)	false
C5	CB	MET- 260	4.36	0	Hydrophobic	false
C15	CE	MET- 260	4.42	0	Hydrophobic	false
C2	CB	MET- 260	4.35	0	Hydrophobic	false
C4	SD	MET- 260	4.12	0	Hydrophobic	false
C20	CG1	VAL- 282	4.46	0	Hydrophobic	false