Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

1fec

1.700 Å

X-ray

1995-07-12

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Trypanothione reductase
ID:TYTR_CRIFA
AC:P39040
Organism:Crithidia fasciculata
Reign:Eukaryota
TaxID:5656
EC Number:1.8.1.12


Chains:

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


Ligand binding site composition:

B-Factor:15.228
Number of residues:82
Including
Standard Amino Acids: 70
Non Standard Amino Acids: 0
Water Molecules: 12
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.2691410.750

% Hydrophobic% Polar
45.4554.55
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median1fecHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
1fec_1 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:80.31 %
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
4.72836-53.3741-12.8412
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median1fecRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80102030Highcharts.com


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
O1ANSER- 133.26166.78H-Bond
(Protein Donor)
C4'CBSER- 134.30Hydrophobic
O1PNGLY- 142.83156.43H-Bond
(Protein Donor)
O3BOD1ASP- 343.35138.24H-Bond
(Ligand Donor)
O3BOD2ASP- 342.95164.33H-Bond
(Ligand Donor)
O2BOD1ASP- 342.72152.42H-Bond
(Ligand Donor)
C3BCBALA- 453.790Hydrophobic
O1ANTHR- 503.04156.85H-Bond
(Protein Donor)
O2AOG1THR- 502.69161.06H-Bond
(Protein Donor)
C8MCG2THR- 503.650Hydrophobic
C2'SGCYS- 564.130Hydrophobic
N5NZLYS- 592.89175.67H-Bond
(Protein Donor)
C6CGLYS- 594.330Hydrophobic
N6AOGLY- 1263.2157.53H-Bond
(Ligand Donor)
N1ANGLY- 1262.86171.11H-Bond
(Protein Donor)
C7MCBSER- 17740Hydrophobic
C7MCE2PHE- 1814.090Hydrophobic
C6CG1ILE- 1984.220Hydrophobic
C9CD1ILE- 1984.170Hydrophobic
C8CD1ILE- 1983.650Hydrophobic
C7MCE2PHE- 2024.380Hydrophobic
C8MCDARG- 2863.970Hydrophobic
O3'OD2ASP- 3263.17133.68H-Bond
(Ligand Donor)
O3'OD1ASP- 3262.88165.85H-Bond
(Ligand Donor)
C5'CBASP- 3264.290Hydrophobic
O2PNASP- 3262.78150.46H-Bond
(Protein Donor)
O2NTHR- 3343150.94H-Bond
(Protein Donor)
C2'CBTHR- 3344.450Hydrophobic
C4'CBTHR- 3344.410Hydrophobic
C5'CBALA- 3374.30Hydrophobic
N3OHIS- 4602.83156.66H-Bond
(Ligand Donor)
O1POHOH- 5212.61172.23H-Bond
(Protein Donor)
O2POHOH- 5232.71179.94H-Bond
(Protein Donor)
O2AOHOH- 5282.73179.95H-Bond
(Protein Donor)
O2BOHOH- 5842.85179.98H-Bond
(Protein Donor)
N6AOHOH- 5933.5123.78H-Bond
(Ligand Donor)