scPDB - 5kbw entry

Protein Data Bank Entry:

PDB ID : 5kbw

Resolution :2.610 Å

Experimental Method : X-ray

Deposition Date : 2016-06-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Riboflavin transporter RibU
ID:	RIBU_THEMA
AC:	Q9X1G6
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	57.746
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.526	388.125

% Hydrophobic	% Polar
47.83	52.17
According to VolSite

Ligand :

HET Code:	RBF
Formula:	C17H20N4O6
Molecular weight:	376.364 g/mol
DrugBank ID:	DB00140
Buried Surface Area:	72.66 %
Polar Surface area:	155.04 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-25.7275	0.0701852	83.1169

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
O4'	OE1	GLU- 24	3.31	150.68	H-Bond (Ligand Donor)	false
C8M	CB	PHE- 33	4.48	0	Hydrophobic	false
C7	CD1	PHE- 33	3.41	0	Hydrophobic	false
C6	CD2	LEU- 34	4.23	0	Hydrophobic	false
C9A	CD2	LEU- 34	4	0	Hydrophobic	false
O2'	N	LYS- 35	2.66	159.34	H-Bond (Protein Donor)	false
O5'	NZ	LYS- 35	3.36	144.48	H-Bond (Protein Donor)	false
C4'	CG	LYS- 35	3.89	0	Hydrophobic	false
C8M	CG1	VAL- 75	4.21	0	Hydrophobic	false
C6	CE	MET- 79	4.37	0	Hydrophobic	false
C9A	CB	MET- 79	4.07	0	Hydrophobic	false
C1'	CB	ASN- 80	4.31	0	Hydrophobic	false
O4	ND2	ASN- 123	2.79	157.13	H-Bond (Protein Donor)	false
C7M	CG2	ILE- 126	3.96	0	Hydrophobic	false
C6	CG2	VAL- 127	4.37	0	Hydrophobic	false
C7M	CG2	VAL- 127	3.72	0	Hydrophobic	false
C7M	CD2	TYR- 130	4.1	0	Hydrophobic	false
C8M	CZ	TYR- 130	3.86	0	Hydrophobic	false
N3	OD1	ASN- 149	2.71	168.85	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 149	2.9	172.79	H-Bond (Protein Donor)	false
O2	NZ	LYS- 152	2.6	151.28	H-Bond (Protein Donor)	false