scPDB - 1y5w entry

Protein Data Bank Entry:

PDB ID : 1y5w

Resolution :1.580 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:	25.265
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.376	442.125

% Hydrophobic	% Polar
45.04	54.96
According to VolSite

Ligand :

HET Code:	NEZ
Formula:	C18H17N5O
Molecular weight:	319.360 g/mol
DrugBank ID:	DB08268
Buried Surface Area:	66.3 %
Polar Surface area:	96.16 Å2

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

Mass center Coordinates

X	Y	Z
15.2411	16.7062	19.484

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
C24	CG1	VAL- 45	3.29	0	Hydrophobic	false
C18	CD2	LEU- 68	3.28	0	Hydrophobic	false
C24	CB	ASN- 70	3.98	0	Hydrophobic	false
N10	OD1	ASP- 102	2.84	166.66	H-Bond (Ligand Donor)	false
N23	OD1	ASP- 102	3.31	135.76	H-Bond (Ligand Donor)	false
N23	OD2	ASP- 102	2.77	145.77	H-Bond (Ligand Donor)	false
C17	CB	ASP- 102	3.97	0	Hydrophobic	false
C15	CD2	TYR- 106	3.29	0	Hydrophobic	false
C5	CG	TYR- 106	3.99	0	Hydrophobic	false
C4	CB	TYR- 106	3.74	0	Hydrophobic	false
DuAr	DuAr	TYR- 106	3.85	0	Aromatic Face/Face	false
N23	OD1	ASP- 156	2.99	150.2	H-Bond (Ligand Donor)	false
C2	SG	CYS- 158	3.86	0	Hydrophobic	false
O22	NE2	GLN- 203	3.07	154.73	H-Bond (Protein Donor)	false
O22	N	GLY- 230	2.89	146.02	H-Bond (Protein Donor)	false
N11	O	LEU- 231	2.82	156.07	H-Bond (Ligand Donor)	false
C4	CB	MET- 260	3.97	0	Hydrophobic	false