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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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PDB Description
Binding Site
Binding Site Similarity
Cavity Similarity
Ligand
Binding Mode
Binding Mode Similarity
Protein Data Bank Entry:

2z1x

1.630 Å

X-ray

2007-05-16

Interactomes:
Interactome scPDB Proteins-Proteins
Interactome scPDB Proteins-Ligands
Interactome scPDB Ligands-Proteins
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Queuine tRNA-ribosyltransferase
ID:TGT_ZYMMO
AC:P28720
Organism:Zymomonas mobilis subsp. mobilis
Reign:Bacteria
TaxID:264203
EC Number:2.4.2.29

Chains:

Chain Name:Percentage of Residues
within binding site
A100 %

Ligand binding site composition:

B-Factor:28.912
Number of residues:30
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.382415.125

% Hydrophobic% Polar
47.9752.03
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2z1xHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
2z1x_1 Structure
HET Code: PRF
Formula: C7H10N5O
Molecular weight: 180.187 g/mol
DrugBank ID: DB03304
Buried Surface Area:73.67 %
Polar Surface area: 110.91 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 4
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
16.693916.835821.3594
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2z1xRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.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
N3OD1ASP- 1022.56170.11H-Bond
(Ligand Donor)
N3OD2ASP- 1023.26126.63H-Bond
(Ligand Donor)
N2OD2ASP- 1022.8143.81H-Bond
(Ligand Donor)
N2OD1ASP- 1562.71163.18H-Bond
(Ligand Donor)
N2OD2ASP- 1563.36129.08H-Bond
(Ligand Donor)
O6NE2GLN- 2033.06158.72H-Bond
(Protein Donor)
O6NGLY- 2302.87140.11H-Bond
(Protein Donor)
N11OMET- 2603.09163.24H-Bond
(Ligand Donor)