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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:

2aly

2.600 Å

X-ray

2005-08-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Phenylalanine--tRNA ligase alpha subunit
ID:SYFA_THETH
AC:P27001
Organism:Thermus thermophilus
Reign:Bacteria
TaxID:274
EC Number:6.1.1.20


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:33.984
Number of residues:44
Including
Standard Amino Acids: 42
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.000668.250

% Hydrophobic% Polar
37.8862.12
According to VolSite

Ligand :
2aly_1 Structure
HET Code: YSA
Formula: C19H23N7O8S
Molecular weight: 509.493 g/mol
DrugBank ID: DB03325
Buried Surface Area:74.06 %
Polar Surface area: 250.09 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 5
Rings: 4
Aromatic rings: 3
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
15.355562.692217.0251


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
NND1HIS- 1783.02153.83H-Bond
(Ligand Donor)
ONH2ARG- 2042.8122.61H-Bond
(Protein Donor)
OADNH2ARG- 2042.68136.28H-Bond
(Protein Donor)
OADNH1ARG- 2042.72134.27H-Bond
(Protein Donor)
O5'NH2ARG- 2043.47141.61H-Bond
(Protein Donor)
N6OE1GLU- 2063.2146.05H-Bond
(Ligand Donor)
N1NGLU- 2132.85171.01H-Bond
(Protein Donor)
N6OGLU- 2132.68127.74H-Bond
(Ligand Donor)
C1'CE2PHE- 2164.190Hydrophobic
DuArDuArPHE- 2163.40Aromatic Face/Face
O4'NE2GLN- 2183.22163.15H-Bond
(Protein Donor)
NOE2GLU- 2203.940Ionic
(Ligand Cationic)
CBCE1PHE- 2583.680Hydrophobic
CD1CE2PHE- 2583.380Hydrophobic
CE1CBPHE- 2584.410Hydrophobic
CBCE2PHE- 2604.420Hydrophobic
CE1CG2VAL- 2614.060Hydrophobic
CZCG1VAL- 2614.380Hydrophobic
CZCBALA- 3144.30Hydrophobic
NOHOH- 10022.74161.36H-Bond
(Ligand Donor)
N7OHOH- 10252.62167.67H-Bond
(Protein Donor)