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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:

2j3n

2.800 Å

X-ray

2006-08-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Thioredoxin reductase 1, cytoplasmic
ID:TRXR1_HUMAN
AC:Q16881
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:1.8.1.9


Chains:

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


Ligand binding site composition:

B-Factor:44.272
Number of residues:69
Including
Standard Amino Acids: 68
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.2851056.375

% Hydrophobic% Polar
47.9252.08
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2j3nHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy80204060Highcharts.com
Ligand :
2j3n_1 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:74.77 %
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
-64.002182.71952.3315
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2j3nRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80102030Highcharts.com


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
C4'CBSER- 224.160Hydrophobic
O1PNGLY- 232.77155.41H-Bond
(Protein Donor)
O3BOD1ASP- 422.9165.64H-Bond
(Ligand Donor)
O2BOPHE- 433.48160.51H-Bond
(Ligand Donor)
N3ANPHE- 433.18156.5H-Bond
(Protein Donor)
O2ANTHR- 582.81161.41H-Bond
(Protein Donor)
C8MCG2THR- 584.190Hydrophobic
C9CG2THR- 584.410Hydrophobic
C2'CBCYS- 594.280Hydrophobic
C2'SGCYS- 644.350Hydrophobic
N5NZLYS- 672.65151.63H-Bond
(Protein Donor)
N6AOGLY- 1323.31175.58H-Bond
(Ligand Donor)
N1ANGLY- 1323.04155.53H-Bond
(Protein Donor)
C7MCBSER- 1803.840Hydrophobic
C8MCBSER- 1804.410Hydrophobic
C7MCZPHE- 1844.380Hydrophobic
C7MCG1VAL- 2013.350Hydrophobic
C7CG2VAL- 2013.340Hydrophobic
C8MCDARG- 2933.980Hydrophobic
O3'OD1ASP- 3342.69152.07H-Bond
(Ligand Donor)
O3'OD2ASP- 3343.04140.62H-Bond
(Ligand Donor)
C5'CBASP- 3344.250Hydrophobic
O2PNASP- 3343.47134.73H-Bond
(Protein Donor)
O2NTHR- 3432.94129.12H-Bond
(Protein Donor)
C2'CBTHR- 3434.230Hydrophobic
C4'CBTHR- 3434.420Hydrophobic
C5'CBALA- 3464.490Hydrophobic
N3OHIS- 4723.07155.12H-Bond
(Ligand Donor)