scPDB - 1bu5 entry

Protein Data Bank Entry:

PDB ID : 1bu5

Resolution :1.830 Å

Experimental Method : X-ray

Deposition Date : 1998-09-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Flavodoxin
ID:	FLAV_DESVH
AC:	P00323
Organism:	Desulfovibrio vulgaris
Reign:	Bacteria
TaxID:	882
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	28.401
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.712	394.875

% Hydrophobic	% Polar
55.56	44.44
According to VolSite

Ligand :

HET Code:	RBF
Formula:	C17H20N4O6
Molecular weight:	376.364 g/mol
DrugBank ID:	DB00140
Buried Surface Area:	55 %
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
15.969	13.1731	11.121

Binding mode :

What is Poseview ?

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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
C5'	CG2	THR- 12	4.26	0	Hydrophobic	false
O2'	O	THR- 59	2.76	163.97	H-Bond (Ligand Donor)	false
C8M	CZ3	TRP- 60	3.62	0	Hydrophobic	false
C2'	CH2	TRP- 60	3.81	0	Hydrophobic	false
N1	N	ASP- 95	3.34	128.93	H-Bond (Protein Donor)	false
O2	N	ASP- 95	2.91	163.27	H-Bond (Protein Donor)	false
C1'	CB	ASP- 95	3.98	0	Hydrophobic	false
C1'	CE2	TYR- 98	3.96	0	Hydrophobic	false
C9A	CZ	TYR- 98	3.48	0	Hydrophobic	false
N3	O	TYR- 100	2.85	176.65	H-Bond (Ligand Donor)	false
O2	N	CYS- 102	2.84	164.7	H-Bond (Protein Donor)	false