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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:

4xoq

2.050 Å

X-ray

2015-01-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Coenzyme F420:L-glutamate ligase
ID:FBIB_MYCTU
AC:P9WP79
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A24 %
B76 %


Ligand binding site composition:

B-Factor:28.714
Number of residues:34
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.2881231.875

% Hydrophobic% Polar
48.2251.78
According to VolSite

Ligand :
4xoq_2 Structure
HET Code: F42
Formula: C29H32N5O18P
Molecular weight: 769.561 g/mol
DrugBank ID: DB03913
Buried Surface Area:55.08 %
Polar Surface area: 389.68 Å2
Number of
H-Bond Acceptors: 20
H-Bond Donors: 7
Rings: 3
Aromatic rings: 1
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 20

Mass center Coordinates

XYZ
47.155217.120643.0165


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
C2ICBHIS- 2903.610Hydrophobic
C6CBLYS- 3164.290Hydrophobic
C7CDLYS- 3164.080Hydrophobic
C2'CZ2TRP- 3173.470Hydrophobic
C6CBTRP- 3173.270Hydrophobic
O8MOD2ASP- 3202.62163.84H-Bond
(Ligand Donor)
C1'CD1PHE- 4033.870Hydrophobic
C3'CE1PHE- 4033.920Hydrophobic
C9CBPHE- 4033.280Hydrophobic