scPDB - 1i5e entry

Protein Data Bank Entry:

PDB ID : 1i5e

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2001-02-27

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_BACCL
AC:	P70881
Organism:	Bacillus caldolyticus
Reign:	Bacteria
TaxID:	1394
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	43.980
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.586	519.750

% Hydrophobic	% Polar
30.52	69.48
According to VolSite

Ligand :

HET Code:	U5P
Formula:	C9H11N2O9P
Molecular weight:	322.165 g/mol
DrugBank ID:	-
Buried Surface Area:	58.58 %
Polar Surface area:	181.33 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
7.20781	64.8902	46.89

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
O2'	OD2	ASP- 131	2.72	162.44	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 131	2.94	170.36	H-Bond (Ligand Donor)	false
C2'	CB	MET- 133	3.82	0	Hydrophobic	false
O2P	N	ALA- 135	2.92	128.2	H-Bond (Protein Donor)	false
O2P	N	THR- 136	2.78	123.11	H-Bond (Protein Donor)	false
O3P	OG1	THR- 136	3.04	166.86	H-Bond (Protein Donor)	false
O3P	N	THR- 136	3.36	166.18	H-Bond (Protein Donor)	false
O2P	N	GLY- 137	2.97	147.47	H-Bond (Protein Donor)	false
C3'	CB	SER- 139	4.48	0	Hydrophobic	false
C5'	CB	SER- 139	4.21	0	Hydrophobic	false
O5'	OG	SER- 139	3.31	142.69	H-Bond (Protein Donor)	false
O1P	N	SER- 139	2.84	165.9	H-Bond (Protein Donor)	false
O1P	OG	SER- 139	2.57	144.46	H-Bond (Protein Donor)	false
O4	N	ILE- 194	2.91	161.12	H-Bond (Protein Donor)	false
N3	O	GLY- 199	2.92	173.89	H-Bond (Ligand Donor)	false
O2	N	ALA- 201	2.97	131.2	H-Bond (Protein Donor)	false
O4	O	HOH- 251	2.98	179.98	H-Bond (Protein Donor)	false