scPDB - 4gkt entry

Protein Data Bank Entry:

PDB ID : 4gkt

Resolution :1.530 Å

Experimental Method : X-ray

Deposition Date : 2012-08-13

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:	20.141
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.843	442.125

% Hydrophobic	% Polar
59.54	40.46
According to VolSite

Ligand :

HET Code:	0O1
Formula:	C25H32N7O
Molecular weight:	446.568 g/mol
DrugBank ID:	-
Buried Surface Area:	60.05 %
Polar Surface area:	124.8 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
15.8718	17.0967	17.549

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
C24	CG1	VAL- 45	3.69	0	Hydrophobic	false
C22	CD2	LEU- 68	3.29	0	Hydrophobic	false
C24	CB	ASN- 70	3.56	0	Hydrophobic	false
N2	OD1	ASP- 102	2.78	166.49	H-Bond (Ligand Donor)	false
N7	OD1	ASP- 102	3.35	131.51	H-Bond (Ligand Donor)	false
N7	OD2	ASP- 102	2.74	146.48	H-Bond (Ligand Donor)	false
C22	CB	ASP- 102	4.36	0	Hydrophobic	false
C3	CG	TYR- 106	3.93	0	Hydrophobic	false
C13	CZ	TYR- 106	4.29	0	Hydrophobic	false
C10	CD1	TYR- 106	3.44	0	Hydrophobic	false
C5	CB	TYR- 106	3.41	0	Hydrophobic	false
N7	OD1	ASP- 156	2.88	149.92	H-Bond (Ligand Donor)	false
C9	SG	CYS- 158	3.49	0	Hydrophobic	false
O1	NE2	GLN- 203	3.05	158.14	H-Bond (Protein Donor)	false
O1	N	GLY- 230	2.8	144.8	H-Bond (Protein Donor)	false
N5	O	LEU- 231	2.82	157.88	H-Bond (Ligand Donor)	false
C15	CB	ALA- 232	4.4	0	Hydrophobic	false
C8	CB	MET- 260	3.99	0	Hydrophobic	false
N1	OD2	ASP- 280	2.68	169.96	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 280	2.68	0	Ionic (Ligand Cationic)	false
N1	OD1	ASP- 280	3.6	0	Ionic (Ligand Cationic)	false
C21	SG	CYS- 281	3.79	0	Hydrophobic	false
C19	CG2	VAL- 282	3.27	0	Hydrophobic	false
C23	CG1	VAL- 282	4.12	0	Hydrophobic	false