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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:

2zz0

2.800 Å

X-ray

2009-02-02

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:39.645
Number of residues:69
Including
Standard Amino Acids: 69
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.719840.375

% Hydrophobic% Polar
35.3464.66
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2zz0HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
2zz0_1 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:74.26 %
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
-50.290822.1551-40.4349
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2zz0RingsAromatic 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
O1ANSER- 223.32162.31H-Bond
(Protein Donor)
C4'CBSER- 224.260Hydrophobic
O1PNGLY- 233.13137.12H-Bond
(Protein Donor)
O3BOD1ASP- 422.95165.97H-Bond
(Ligand Donor)
O2BOPHE- 432.86160.89H-Bond
(Ligand Donor)
N3ANPHE- 432.74149.21H-Bond
(Protein Donor)
O1ANTHR- 583.35153.34H-Bond
(Protein Donor)
O2ANTHR- 583.13142.28H-Bond
(Protein Donor)
O2AOG1THR- 583.04144.7H-Bond
(Protein Donor)
C8MCG2THR- 583.610Hydrophobic
C2'SGCYS- 644.480Hydrophobic
N5NZLYS- 673.23145.07H-Bond
(Protein Donor)
C6CBLYS- 674.390Hydrophobic
N6AOGLY- 1323159.93H-Bond
(Ligand Donor)
N1ANGLY- 1323.04159.47H-Bond
(Protein Donor)
C7MCBSER- 1803.930Hydrophobic
C7MCE2PHE- 1844.070Hydrophobic
C7MCG2VAL- 2013.750Hydrophobic
C8CG2VAL- 2014.190Hydrophobic
C8MCDARG- 2933.950Hydrophobic
O3'OD1ASP- 3342.8162.54H-Bond
(Ligand Donor)
O3'OD2ASP- 3343.25127.01H-Bond
(Ligand Donor)
C5'CBASP- 3344.490Hydrophobic
O2PNASP- 3343.01144.11H-Bond
(Protein Donor)
O2NTHR- 3433.03123.91H-Bond
(Protein Donor)
C2'CBTHR- 3434.440Hydrophobic
C4'CBTHR- 3434.420Hydrophobic
C5'CBALA- 3464.480Hydrophobic
N3OHIS- 4722.92140.91H-Bond
(Ligand Donor)