scPDB - 1u1f entry

Protein Data Bank Entry:

PDB ID : 1u1f

Resolution :2.300 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
C	16 %
D	84 %

Ligand binding site composition:

B-Factor:	15.857
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.469	614.250

% Hydrophobic	% Polar
45.05	54.95
According to VolSite

Ligand :

HET Code:	183
Formula:	C21H22N2O5
Molecular weight:	382.410 g/mol
DrugBank ID:	DB06873
Buried Surface Area:	66.07 %
Polar Surface area:	88.1 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
32.4258	208.891	50.7807

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
CAL	CB	PHE- 7	4.35	0	Hydrophobic	false
CAP	CB	PHE- 7	4.35	0	Hydrophobic	false
CAI	CB	PHE- 7	4.46	0	Hydrophobic	false
OAC	NE2	HIS- 8	2.65	173.37	H-Bond (Ligand Donor)	false
CAN	CD1	ILE- 69	3.8	0	Hydrophobic	false
CAO	CD1	PHE- 162	3.98	0	Hydrophobic	false
OAB	NE2	GLN- 166	2.76	157.49	H-Bond (Protein Donor)	false
NAS	OE1	GLN- 166	2.75	170.95	H-Bond (Ligand Donor)	false
OAA	NH1	ARG- 168	3.47	131.87	H-Bond (Protein Donor)	false
OAA	NH2	ARG- 168	2.82	171.62	H-Bond (Protein Donor)	false
CAR	CB	GLU- 196	4.46	0	Hydrophobic	false
CAO	SD	MET- 197	3.93	0	Hydrophobic	false
CAQ	CG1	ILE- 220	3.69	0	Hydrophobic	false
CAJ	CD1	ILE- 220	4.16	0	Hydrophobic	false
CAM	CD1	ILE- 220	3.74	0	Hydrophobic	false
CAK	CG1	VAL- 221	3.8	0	Hydrophobic	false
CAQ	CB	VAL- 221	4.23	0	Hydrophobic	false
CAJ	CG	PRO- 229	4.26	0	Hydrophobic	false
CAG	CB	PRO- 229	3.81	0	Hydrophobic	false
CAE	CG	PRO- 229	3.8	0	Hydrophobic	false
CAH	CG	PRO- 229	3.74	0	Hydrophobic	false
CAG	SD	MET- 234	3.78	0	Hydrophobic	false
OAA	O	HOH- 6327	2.63	142.28	H-Bond (Protein Donor)	false