scPDB - 1jlr entry

Protein Data Bank Entry:

PDB ID : 1jlr

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2001-07-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uracil phosphoribosyltransferase
ID:	UPP_TOXGO
AC:	Q26998
Organism:	Toxoplasma gondii
Reign:	Eukaryota
TaxID:	5811
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	72 %
C	21 %
D	7 %

Ligand binding site composition:

B-Factor:	22.096
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.136	394.875

% Hydrophobic	% Polar
34.19	65.81
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	45.63 %
Polar Surface area:	335.56 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
15.2725	90.9582	76.1363

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
O1G	NZ	LYS- 59	2.77	126.61	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 59	3.2	150.83	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 59	2.77	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 59	3.2	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 59	3.75	0	Ionic (Protein Cationic)	false
N7	NH1	ARG- 68	3.01	143.04	H-Bond (Protein Donor)	false
O6	NH2	ARG- 68	2.91	161.32	H-Bond (Protein Donor)	false
C2'	CD1	PHE- 101	4.05	0	Hydrophobic	false
O2B	NZ	LYS- 104	2.84	171.66	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 104	2.84	0	Ionic (Protein Cationic)	false
C5'	CG1	ILE- 105	4.03	0	Hydrophobic	false
O1G	NH1	ARG- 129	3.25	136.16	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 129	3.83	0	Ionic (Protein Cationic)	false
O1B	NH1	ARG- 158	3.42	140.82	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 158	3.4	141.62	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 158	3.38	148.16	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 158	3.83	0	Ionic (Protein Cationic)	false
O2A	O	HOH- 807	2.59	179.99	H-Bond (Protein Donor)	false