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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:

3fwy

1.630 Å

X-ray

2009-01-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
ID:BCHL_RHOS4
AC:Q9RFD6
Organism:Rhodobacter sphaeroides
Reign:Bacteria
TaxID:272943
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A94 %
B6 %


Ligand binding site composition:

B-Factor:18.471
Number of residues:37
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.327698.625

% Hydrophobic% Polar
41.0658.94
According to VolSite

Ligand :
3fwy_1 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:67.85 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-4.0983745.735171.6228


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
O2BNGLY- 412.93132.96H-Bond
(Protein Donor)
O1BNGLY- 432.97150.68H-Bond
(Protein Donor)
O3ANGLY- 433.22129.53H-Bond
(Protein Donor)
O1BNLYS- 442.8156.62H-Bond
(Protein Donor)
O1BNZLYS- 442.87161.38H-Bond
(Protein Donor)
O1BNZLYS- 442.870Ionic
(Protein Cationic)
O2BNZLYS- 443.730Ionic
(Protein Cationic)
O3BNSER- 452.97153.24H-Bond
(Protein Donor)
O2ANTHR- 462.81152.39H-Bond
(Protein Donor)
O2AOG1THR- 462.65157.91H-Bond
(Protein Donor)
O2BNZLYS- 702.8154.04H-Bond
(Protein Donor)
O2BNZLYS- 702.80Ionic
(Protein Cationic)
N7ND2ASN- 2113163.29H-Bond
(Protein Donor)
N6OD1ASN- 2112.91162.8H-Bond
(Ligand Donor)
O4'NH1ARG- 2122.97126.84H-Bond
(Protein Donor)
N6OPRO- 2352.88155.84H-Bond
(Ligand Donor)
N1NLEU- 2373.03162.57H-Bond
(Protein Donor)
O3BMG MG- 4012.060Metal Acceptor