scPDB - 3upy entry

Protein Data Bank Entry:

PDB ID : 3upy

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2011-11-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Oxidoreductase, putative
ID:	Q2YIM3_BRUA2
AC:	Q2YIM3
Organism:	Brucella abortus
Reign:	Bacteria
TaxID:	359391
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	95 %
B	5 %

Ligand binding site composition:

B-Factor:	17.539
Number of residues:	23
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.988	1485.000

% Hydrophobic	% Polar
43.86	56.14
According to VolSite

Ligand :

HET Code:	FOM
Formula:	C4H8NO5P
Molecular weight:	181.084 g/mol
DrugBank ID:	DB02948
Buried Surface Area:	60.31 %
Polar Surface area:	113.54 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
9.86682	-7.205	15.789

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
O2	OE2	GLU- 168	2.58	157.66	H-Bond (Ligand Donor)	false
OP1	NZ	LYS- 191	2.88	0	Ionic (Protein Cationic)	false
OP2	NZ	LYS- 191	2.63	0	Ionic (Protein Cationic)	false
OP2	NZ	LYS- 191	2.63	171.89	H-Bond (Protein Donor)	false
OP3	NZ	LYS- 193	2.81	156.01	H-Bond (Protein Donor)	false
OP3	NZ	LYS- 193	2.81	0	Ionic (Protein Cationic)	false
C3	CD1	PHE- 223	3.57	0	Hydrophobic	false
C4	CG	PHE- 223	3.51	0	Hydrophobic	false
C3	CG	LYS- 228	4.37	0	Hydrophobic	false
O2	MG	MG- 446	2.01	0	Metal Acceptor	false
O1	MG	MG- 446	1.91	0	Metal Acceptor	false
OP1	O	HOH- 491	2.79	179.97	H-Bond (Protein Donor)	false