scPDB - 1i3l entry

Protein Data Bank Entry:

PDB ID : 1i3l

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2001-02-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-glucose 4-epimerase
ID:	GALE_HUMAN
AC:	Q14376
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	29.377
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.775	1032.750

% Hydrophobic	% Polar
38.24	61.76
According to VolSite

Ligand :

HET Code:	GDU
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB03501
Buried Surface Area:	55.97 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
24.5512	17.9792	48.8417

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
O2B	ND2	ASN- 187	2.67	154.09	H-Bond (Protein Donor)	false
C1D	CD1	LEU- 208	4.45	0	Hydrophobic	false
C4D	CD2	LEU- 208	4.37	0	Hydrophobic	false
C5D	CB	LEU- 208	4.1	0	Hydrophobic	false
O1A	N	LEU- 208	2.89	174.76	H-Bond (Protein Donor)	false
N3	O	ASN- 224	2.94	173.86	H-Bond (Ligand Donor)	false
O2	N	PHE- 226	2.73	171.93	H-Bond (Protein Donor)	false
C2D	CD1	PHE- 226	4.11	0	Hydrophobic	false
O1B	CZ	ARG- 239	3.67	0	Ionic (Protein Cationic)	false
O1B	NE	ARG- 239	3.11	159.38	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 239	3.31	144.15	H-Bond (Protein Donor)	false
C5D	CG	ARG- 239	3.93	0	Hydrophobic	false
C1D	CG2	VAL- 277	3.79	0	Hydrophobic	false
C4D	CG2	VAL- 277	4.12	0	Hydrophobic	false
O5D	NH2	ARG- 300	3.22	131.96	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 300	2.68	158.17	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 300	3.15	133.47	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 300	3.37	0	Ionic (Protein Cationic)	false
O2D	OD2	ASP- 303	2.52	148.76	H-Bond (Ligand Donor)	false