scPDB - 2wsi entry

Protein Data Bank Entry:

PDB ID : 2wsi

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2009-09-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	FAD synthase
ID:	FAD1_YEAST
AC:	P38913
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	2.7.7.2

Chains:

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

Ligand binding site composition:

B-Factor:	20.256
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.663	884.250

% Hydrophobic	% Polar
37.02	62.98
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	56.98 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
24.8818	20.6499	23.8362

Binding mode :

What is Poseview ?

2D View
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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
O2B	OG	SER- 59	3.14	169.86	H-Bond (Ligand Donor)	false
C1B	CB	SER- 59	4.29	0	Hydrophobic	false
N7A	ND2	ASN- 61	3.29	134.8	H-Bond (Protein Donor)	false
C2B	CB	CYS- 66	4.19	0	Hydrophobic	false
N6A	O	ILE- 107	2.91	169.47	H-Bond (Ligand Donor)	false
N1A	N	ILE- 107	2.9	170.02	H-Bond (Protein Donor)	false
C8M	CE	MET- 144	3.87	0	Hydrophobic	false
C7M	CZ	PHE- 148	3.66	0	Hydrophobic	false
C8M	CE1	PHE- 148	4.16	0	Hydrophobic	false
C7M	CG2	ILE- 161	4.07	0	Hydrophobic	false
C1B	CG2	ILE- 163	4.31	0	Hydrophobic	false
C8M	CG2	ILE- 163	4.39	0	Hydrophobic	false
C4B	CG2	ILE- 163	3.56	0	Hydrophobic	false
C7	CD1	ILE- 163	3.52	0	Hydrophobic	false
O3B	O	GLY- 164	3.38	136.57	H-Bond (Ligand Donor)	false
O2B	N	GLY- 164	2.96	176.98	H-Bond (Protein Donor)	false
C5B	CB	ILE- 165	4.23	0	Hydrophobic	false
C3'	CD1	ILE- 165	3.86	0	Hydrophobic	false
N3	OD2	ASP- 182	2.63	141.18	H-Bond (Ligand Donor)	false
O4	N	ASP- 182	2.82	166.39	H-Bond (Protein Donor)	false
C7M	CZ3	TRP- 185	4.23	0	Hydrophobic	false
C1'	CZ2	TRP- 185	3.99	0	Hydrophobic	false
DuAr	DuAr	TRP- 185	3.69	0	Aromatic Face/Face	false
C7M	CZ	PHE- 188	3.95	0	Hydrophobic	false
C6	CD	ARG- 190	4.29	0	Hydrophobic	false
O1P	NH1	ARG- 300	2.78	125.63	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 300	3.58	0	Ionic (Protein Cationic)	false