scPDB - 1u1d entry

Protein Data Bank Entry:

PDB ID : 1u1d

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2004-07-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uridine phosphorylase
ID:	UDP_ECOLI
AC:	P12758
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.4.2.3

Chains:

Chain Name:	Percentage of Residues within binding site
E	84 %
F	16 %

Ligand binding site composition:

B-Factor:	16.757
Number of residues:	27
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.727	968.625

% Hydrophobic	% Polar
42.86	57.14
According to VolSite

Ligand :

HET Code:	181
Formula:	C13H14N2O4S
Molecular weight:	294.326 g/mol
DrugBank ID:	DB06872
Buried Surface Area:	69.4 %
Polar Surface area:	104.17 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-9.9446	204.167	-20.384

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
CAD	CB	PHE- 7	4.16	0	Hydrophobic	false
OAC	NE2	HIS- 8	2.75	158.85	H-Bond (Ligand Donor)	false
CAJ	CD1	ILE- 69	3.8	0	Hydrophobic	false
CAK	CD1	PHE- 162	4.28	0	Hydrophobic	false
OAB	NE2	GLN- 166	2.76	155.05	H-Bond (Protein Donor)	false
NAM	OE1	GLN- 166	2.69	178.03	H-Bond (Ligand Donor)	false
OAA	NH1	ARG- 168	3.44	131.39	H-Bond (Protein Donor)	false
OAA	NH2	ARG- 168	2.81	167.55	H-Bond (Protein Donor)	false
CAL	CB	GLU- 196	4.43	0	Hydrophobic	false
CAK	SD	MET- 197	3.93	0	Hydrophobic	false
CAG	CD1	ILE- 220	3.78	0	Hydrophobic	false
SAO	CD1	ILE- 220	3.74	0	Hydrophobic	false
CAH	CG1	VAL- 221	3.78	0	Hydrophobic	false
SAO	CG1	VAL- 221	3.73	0	Hydrophobic	false
CAF	CG	PRO- 229	4.2	0	Hydrophobic	false
OAA	O	HOH- 7436	2.74	141.62	H-Bond (Protein Donor)	false