Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3g5h

1.400 Å

X-ray

2009-02-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Mycocyclosin synthase
ID:CP121_MYCTU
AC:P9WPP7
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:1.14.21.9


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:8.915
Number of residues:30
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.3231447.875

% Hydrophobic% Polar
51.7548.25
According to VolSite

Ligand :
3g5h_1 Structure
HET Code: YTT
Formula: C18H18N2O4
Molecular weight: 326.347 g/mol
DrugBank ID: DB08761
Buried Surface Area:58.33 %
Polar Surface area: 98.66 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
9.050518.3994-2.46837


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
CBACEMET- 624.070Hydrophobic
CE4CG1VAL- 783.530Hydrophobic
OBND2ASN- 852.97153.45H-Bond
(Protein Donor)
CD3CBTHR- 2293.770Hydrophobic
CE3CG2THR- 2294.230Hydrophobic
CBBCBALA- 2334.230Hydrophobic
CD3CBALA- 2334.390Hydrophobic
OHAOHOH- 7292.84179.95H-Bond
(Protein Donor)