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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:

1akr

1.580 Å

X-ray

1997-05-27

Interactomes:
Molecular Function:
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
A100 %


Ligand binding site composition:

B-Factor:24.241
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.638381.375

% Hydrophobic% Polar
51.3348.67
According to VolSite

Ligand :
1akr_1 Structure
HET Code: FMN
Formula: C17H19N4O9P
Molecular weight: 454.328 g/mol
DrugBank ID: DB03247
Buried Surface Area:66.17 %
Polar Surface area: 217.05 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 4
Rings: 3
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
-5.3901333.276517.2105


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
O2POGSER- 102.52144.54H-Bond
(Protein Donor)
O1PNTHR- 112.7167.11H-Bond
(Protein Donor)
O1PNTHR- 123.43158.46H-Bond
(Protein Donor)
O3PNTHR- 122.84127.65H-Bond
(Protein Donor)
O3POG1THR- 122.51177.35H-Bond
(Protein Donor)
O4'ND2ASN- 142.8174.7H-Bond
(Protein Donor)
O3PNASN- 142.79163.66H-Bond
(Protein Donor)
O2PNTHR- 152.52159.15H-Bond
(Protein Donor)
O2POG1THR- 152.69142.56H-Bond
(Protein Donor)
O1POGSER- 582.59160.23H-Bond
(Protein Donor)
C5'CBSER- 583.610Hydrophobic
O2'OTHR- 592.8160.01H-Bond
(Ligand Donor)
C7MCE3TRP- 604.230Hydrophobic
C2'CZ2TRP- 604.450Hydrophobic
C5'CZ2TRP- 603.850Hydrophobic
C8CZ3TRP- 603.380Hydrophobic
N5NALA- 612.97168.76H-Bond
(Protein Donor)
C6CBALA- 614.420Hydrophobic
C4'CBCYS- 933.930Hydrophobic
O2NASP- 952.89162H-Bond
(Protein Donor)
C1'CBASP- 953.660Hydrophobic
C1'CE1TYR- 984.260Hydrophobic
N3OTYR- 1002.96170H-Bond
(Ligand Donor)
O2NCYS- 1022.81171.46H-Bond
(Protein Donor)
O4'OHOH- 1532.65164.76H-Bond
(Ligand Donor)