scPDB - 3ex8 entry

Protein Data Bank Entry:

PDB ID : 3ex8

Resolution :2.560 Å

Experimental Method : X-ray

Deposition Date : 2008-10-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Riboflavin biosynthesis protein RibD
ID:	RIBD_BACSU
AC:	P17618
Organism:	Bacillus subtilis
Reign:	Bacteria
TaxID:	224308
EC Number:	1.1.1.193

Chains:

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

Ligand binding site composition:

B-Factor:	64.029
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.361	823.500

% Hydrophobic	% Polar
38.52	61.48
According to VolSite

Ligand :

HET Code:	AIF
Formula:	C9H13N4O9P
Molecular weight:	352.195 g/mol
DrugBank ID:	-
Buried Surface Area:	54.81 %
Polar Surface area:	239.49 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	6
Rings:	1
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
44.327	55.6758	77.3911

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	NZ	LYS- 151	3.37	125.96	H-Bond (Protein Donor)	false
O4	N	ILE- 170	3.15	136.62	H-Bond (Protein Donor)	false
O4	N	THR- 171	3.12	153.97	H-Bond (Protein Donor)	false
O1P	NH1	ARG- 183	3.29	137.61	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 183	2.65	150.11	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 183	2.68	171.29	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 183	3.52	0	Ionic (Protein Cationic)	false
C3'	CB	ASP- 199	4.36	0	Hydrophobic	false
O3'	OD2	ASP- 199	2.76	162.27	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 199	3.11	147.72	H-Bond (Ligand Donor)	false
C5'	CB	PRO- 201	3.61	0	Hydrophobic	false
O3P	N	SER- 202	3.44	142.13	H-Bond (Protein Donor)	false
O3P	N	LEU- 203	2.7	138.86	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 206	3.77	0	Ionic (Protein Cationic)	false
O4'	OE2	GLU- 290	2.7	151.53	H-Bond (Ligand Donor)	false