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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:

1n2v

2.100 Å

X-ray

2002-10-24

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:4.0804.0804.0800.0004.0801

List of CHEMBLId :

CHEMBL280051


Interactomes:
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:32.004
Number of residues:32
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 4
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.550384.750

% Hydrophobic% Polar
42.9857.02
According to VolSite

Ligand :
1n2v_1 Structure
HET Code: BDI
Formula: C9H12N4O2
Molecular weight: 208.217 g/mol
DrugBank ID: DB02441
Buried Surface Area:59.02 %
Polar Surface area: 86.88 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 3
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
16.228717.404320.8774


Binding mode :
What is Poseview ?
  • 2D View
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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
C6CE1TYR- 1064.450Hydrophobic
C7CE2TYR- 1063.710Hydrophobic
C8CZTYR- 1063.950Hydrophobic
C9CE2TYR- 1063.860Hydrophobic
N5OD2ASP- 1562.68154.96H-Bond
(Ligand Donor)
N4OD1ASP- 1562.77133.25H-Bond
(Ligand Donor)
O3NE2GLN- 2033.22160H-Bond
(Protein Donor)
O3NGLY- 2302.73143.7H-Bond
(Protein Donor)
C6CBALA- 2324.030Hydrophobic
C8CBALA- 2323.960Hydrophobic
C6CBMET- 2604.190Hydrophobic
N1OHOH- 14013.1167.6H-Bond
(Ligand Donor)
O1OHOH- 14042.63160.61H-Bond
(Protein Donor)