scPDB - 3ukf entry

Protein Data Bank Entry:

PDB ID : 3ukf

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2011-11-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-galactopyranose mutase
ID:	Q4W1X2_ASPFM
AC:	Q4W1X2
Organism:	Neosartorya fumigata
Reign:	Eukaryota
TaxID:	746128
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	64.899
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.946	1539.000

% Hydrophobic	% Polar
41.89	58.11
According to VolSite

Ligand :

HET Code:	GDU
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB03501
Buried Surface Area:	66.18 %
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
-13.0035	55.5312	36.1125

Binding mode :

What is Poseview ?

2D View
3D View

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
O6'	O	GLY- 62	2.85	136.57	H-Bond (Ligand Donor)	false
C6'	CG2	VAL- 64	4.34	0	Hydrophobic	false
O4	N	PHE- 106	2.87	176.49	H-Bond (Protein Donor)	false
N3	OE1	GLN- 107	3.05	170.11	H-Bond (Ligand Donor)	false
O2	NE2	GLN- 107	3.18	166.83	H-Bond (Protein Donor)	false
C2D	CE2	TYR- 162	4.06	0	Hydrophobic	false
O2D	ND2	ASN- 163	3.44	128.59	H-Bond (Protein Donor)	false
O2D	OD1	ASN- 163	2.83	164.97	H-Bond (Ligand Donor)	false
O3D	OD1	ASN- 163	2.94	165.08	H-Bond (Ligand Donor)	false
O3D	NE1	TRP- 167	3.09	142.65	H-Bond (Protein Donor)	false
C4D	CB	ARG- 182	4.4	0	Hydrophobic	false
O2'	NH1	ARG- 182	3.28	134.23	H-Bond (Protein Donor)	false
C1D	CG2	VAL- 183	4.1	0	Hydrophobic	false
O4'	ND2	ASN- 207	3.39	122.41	H-Bond (Protein Donor)	false
C6'	CE2	TRP- 315	4.14	0	Hydrophobic	false
O1A	OH	TYR- 317	3.34	152.27	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 327	2.63	163.7	H-Bond (Protein Donor)	false
O5'	NH1	ARG- 327	2.88	125.19	H-Bond (Protein Donor)	false
O1B	OH	TYR- 419	3.11	162.73	H-Bond (Protein Donor)	false
O2B	OH	TYR- 453	2.91	168.94	H-Bond (Protein Donor)	false
O2B	O	HOH- 528	3.16	158.24	H-Bond (Protein Donor)	false