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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:

1jay

1.650 Å

X-ray

2001-06-01

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:F420-dependent NADP reductase
ID:FNO_ARCFU
AC:O29370
Organism:Archaeoglobus fulgidus
Reign:Archaea
TaxID:224325
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:18.287
Number of residues:22
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: NAP
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.824340.875

% Hydrophobic% Polar
55.4544.55
According to VolSite

Ligand :
1jay_2 Structure
HET Code: F42
Formula: C29H32N5O18P
Molecular weight: 769.561 g/mol
DrugBank ID: DB03913
Buried Surface Area:26.25 %
Polar Surface area: 389.68 Å2
Number of
H-Bond Acceptors: 20
H-Bond Donors: 7
Rings: 3
Aromatic rings: 1
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 20

Mass center Coordinates

XYZ
-5.1916228.4376-1.47474


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
C8CBPRO- 1363.530Hydrophobic
C5ACG2THR- 1923.930Hydrophobic
C8CG2ILE- 1953.990Hydrophobic
C1'CD2LEU- 1963.70Hydrophobic
C9CD2LEU- 1963.930Hydrophobic
C9SDMET- 1994.120Hydrophobic
O3'OE2GLU- 2063.27156.66H-Bond
(Ligand Donor)
O8MNLEU- 2072.83146.31H-Bond
(Protein Donor)
O8MOLEU- 2072.67160.35H-Bond
(Ligand Donor)
O4O2DNAP- 2132.6164.8H-Bond
(Protein Donor)
O2'O7NNAP- 2132.87152.58H-Bond
(Ligand Donor)