Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4cqn

2.500 Å

X-ray

2014-02-20

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Leucine--tRNA ligase
ID:SYL_ECOLI
AC:P07813
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:88.871
Number of residues:26
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.4871981.125

% Hydrophobic% Polar
35.6064.40
According to VolSite

Ligand :
4cqn_4 Structure
HET Code: ILA
Formula: C16H27N8O6S
Molecular weight: 459.501 g/mol
DrugBank ID: DB01755
Buried Surface Area:52.5 %
Polar Surface area: 230.59 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 6
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-15.168324.9748-99.1413


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
C5'CE2TYR- 2464.050Hydrophobic
NOG1THR- 2472.68137.54H-Bond
(Ligand Donor)
O1AOG1THR- 2483.19158.48H-Bond
(Protein Donor)
C1'CBTYR- 3304.390Hydrophobic
CBSDMET- 3363.910Hydrophobic
CDCEMET- 3363.750Hydrophobic
CDCBVAL- 3383.750Hydrophobic
CG2CBASP- 3424.270Hydrophobic
CG1CBASP- 3423.540Hydrophobic
O2ANH2ARG- 3442.78133.3H-Bond
(Protein Donor)