scPDB - 2z1w entry

Protein Data Bank Entry:

PDB ID : 2z1w

Resolution :1.630 Å

Experimental Method : X-ray

Deposition Date : 2007-05-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	4.080	4.080	4.080	0.000	4.080	1

List of CHEMBLId :

CHEMBL280051

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:	22.243
Number of residues:	29
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.811	401.625

% Hydrophobic	% Polar
52.10	47.90
According to VolSite

Ligand :

HET Code:	BDI
Formula:	C9H12N4O2
Molecular weight:	208.217 g/mol
DrugBank ID:	DB02441
Buried Surface Area:	62.73 %
Polar Surface area:	86.88 Å2

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

Mass center Coordinates

X	Y	Z
16.3241	17.5033	21.0174

Binding mode :

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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
C9	CZ	TYR- 106	3.51	0	Hydrophobic	false
N5	OD2	ASP- 156	2.54	152.96	H-Bond (Ligand Donor)	false
N4	OD1	ASP- 156	2.74	135.74	H-Bond (Ligand Donor)	false
O3	NE2	GLN- 203	2.98	159.19	H-Bond (Protein Donor)	false
O3	N	GLY- 230	2.79	129.53	H-Bond (Protein Donor)	false
C8	CB	ALA- 232	4.06	0	Hydrophobic	false
C6	CB	MET- 260	4.25	0	Hydrophobic	false
O1	O	HOH- 961	2.72	161.83	H-Bond (Protein Donor)	false