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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:

4xt8

1.950 Å

X-ray

2015-01-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc
ID:P71968_MYCTU
AC:P71968
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:20.665
Number of residues:36
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors: NAP
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.382367.875

% Hydrophobic% Polar
45.8754.13
According to VolSite

Ligand :
4xt8_1 Structure
HET Code: TMQ
Formula: C19H23N5O3
Molecular weight: 369.418 g/mol
DrugBank ID: DB01157
Buried Surface Area:66.13 %
Polar Surface area: 117.54 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
17.93926.36221.5083


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
N24OD1ASN- 442.99142.52H-Bond
(Ligand Donor)
N25OASN- 442.68166.55H-Bond
(Ligand Donor)
C4ACG2ILE- 463.990Hydrophobic
C8CG2ILE- 463.920Hydrophobic
C9CBSER- 594.20Hydrophobic
C5CBSER- 594.090Hydrophobic
C6CBSER- 593.930Hydrophobic
C8CBALA- 633.630Hydrophobic
N1OD1ASP- 673.31130.49H-Bond
(Ligand Donor)
N1OD2ASP- 672.54162.9H-Bond
(Ligand Donor)
N24OD1ASP- 672.74163.14H-Bond
(Ligand Donor)
C21CGARG- 684.120Hydrophobic
C17CE2PHE- 714.120Hydrophobic
C21CD1PHE- 713.410Hydrophobic
C22CE1PHE- 713.450Hydrophobic
C4ACE2PHE- 713.450Hydrophobic
C9CGGLU- 914.130Hydrophobic
C16CBGLU- 914.290Hydrophobic
N25OGLU- 1933.16122.49H-Bond
(Ligand Donor)
N24OG1THR- 2143.28128.05H-Bond
(Ligand Donor)
C17C4NNAP- 3013.730Hydrophobic
O20OHOH- 4523.11179.98H-Bond
(Protein Donor)