scPDB - 3gf4 entry

Protein Data Bank Entry:

PDB ID : 3gf4

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2009-02-26

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:	GLF1_KLEPN
AC:	Q48485
Organism:	Klebsiella pneumoniae
Reign:	Bacteria
TaxID:	573
EC Number:	5.4.99.9

Chains:

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

Ligand binding site composition:

B-Factor:	39.911
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.688	941.625

% Hydrophobic	% Polar
46.59	53.41
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	67.46 %
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
-26.7472	-41.9483	-0.723

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
C1C	CE1	PHE- 135	4.35	0	Hydrophobic	false
N3	O	PHE- 151	2.96	157.26	H-Bond (Ligand Donor)	false
C1C	CD2	PHE- 152	4.22	0	Hydrophobic	false
C3C	CE2	TYR- 155	4.18	0	Hydrophobic	false
C2C	CD2	TYR- 155	3.68	0	Hydrophobic	false
O2C	OG1	THR- 156	2.67	163.34	H-Bond (Ligand Donor)	false
O2C	NE1	TRP- 160	3.45	136.04	H-Bond (Protein Donor)	false
O3C	NE1	TRP- 160	2.9	146.24	H-Bond (Protein Donor)	false
C4C	CG2	ILE- 171	3.6	0	Hydrophobic	false
C5C	CD1	LEU- 175	3.86	0	Hydrophobic	false
O1A	OH	TYR- 185	2.7	146.18	H-Bond (Protein Donor)	false
O2A	OH	TYR- 185	3.5	143.23	H-Bond (Protein Donor)	false
C5'	CE2	TYR- 185	4.11	0	Hydrophobic	false
C6'	CZ	TYR- 185	3.63	0	Hydrophobic	false
O4	ND2	ASN- 270	2.97	154.05	H-Bond (Protein Donor)	false
O2'	OH	TYR- 314	2.53	137.83	H-Bond (Protein Donor)	false
C2'	C6	FAD- 391	4.36	0	Hydrophobic	false
O3'	N5	FAD- 391	2.86	145.69	H-Bond (Ligand Donor)	false