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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

2wsi

1.900 Å

X-ray

2009-09-07

Interactomes:
Molecular Function:
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
A100 %


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

LigandabilityVolume (Å3)
0.663884.250

% Hydrophobic% Polar
37.0262.98
According to VolSite

Ligand :
2wsi_1 Structure
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

XYZ
24.881820.649923.8362


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
O2BOGSER- 593.14169.86H-Bond
(Ligand Donor)
C1BCBSER- 594.290Hydrophobic
N7AND2ASN- 613.29134.8H-Bond
(Protein Donor)
C2BCBCYS- 664.190Hydrophobic
N6AOILE- 1072.91169.47H-Bond
(Ligand Donor)
N1ANILE- 1072.9170.02H-Bond
(Protein Donor)
C8MCEMET- 1443.870Hydrophobic
C7MCZPHE- 1483.660Hydrophobic
C8MCE1PHE- 1484.160Hydrophobic
C7MCG2ILE- 1614.070Hydrophobic
C1BCG2ILE- 1634.310Hydrophobic
C8MCG2ILE- 1634.390Hydrophobic
C4BCG2ILE- 1633.560Hydrophobic
C7CD1ILE- 1633.520Hydrophobic
O3BOGLY- 1643.38136.57H-Bond
(Ligand Donor)
O2BNGLY- 1642.96176.98H-Bond
(Protein Donor)
C5BCBILE- 1654.230Hydrophobic
C3'CD1ILE- 1653.860Hydrophobic
N3OD2ASP- 1822.63141.18H-Bond
(Ligand Donor)
O4NASP- 1822.82166.39H-Bond
(Protein Donor)
C7MCZ3TRP- 1854.230Hydrophobic
C1'CZ2TRP- 1853.990Hydrophobic
DuArDuArTRP- 1853.690Aromatic Face/Face
C7MCZPHE- 1883.950Hydrophobic
C6CDARG- 1904.290Hydrophobic
O1PNH1ARG- 3002.78125.63H-Bond
(Protein Donor)
O1PCZARG- 3003.580Ionic
(Protein Cationic)