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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:

1gl3

2.600 Å

X-ray

2001-08-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aspartate-semialdehyde dehydrogenase
ID:DHAS_ECOLI
AC:P0A9Q9
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A91 %
B9 %


Ligand binding site composition:

B-Factor:28.318
Number of residues:53
Including
Standard Amino Acids: 53
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.331428.625

% Hydrophobic% Polar
28.3571.65
According to VolSite

Ligand :
1gl3_1 Structure
HET Code: NDP
Formula: C21H26N7O17P3
Molecular weight: 741.389 g/mol
DrugBank ID: DB02338
Buried Surface Area:62.28 %
Polar Surface area: 404.9 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 5
Rings: 5
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
-0.9177551.3411.5007


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
O1XCZARG- 103.680Ionic
(Protein Cationic)
O1XNH1ARG- 102.92131.49H-Bond
(Protein Donor)
O1ANMET- 123.17172.11H-Bond
(Protein Donor)
O2NNVAL- 132.67165.2H-Bond
(Protein Donor)
C5DCG2VAL- 134.440Hydrophobic
C3NCG2VAL- 133.790Hydrophobic
O2XNTHR- 373.4138.45H-Bond
(Protein Donor)
O2XOG1THR- 372.8150.68H-Bond
(Protein Donor)
O3XOGSER- 382.53160.85H-Bond
(Protein Donor)
O2XNE2GLN- 733.17157.37H-Bond
(Protein Donor)
C4NCBCYS- 1353.710Hydrophobic
N7NOSER- 1652.66156.99H-Bond
(Ligand Donor)
O1ANALA- 1693.12168.5H-Bond
(Protein Donor)
O7NNE2GLN- 3503.03140.09H-Bond
(Protein Donor)
C4NCGGLN- 3504.430Hydrophobic
C5NCBALA- 3553.740Hydrophobic
C4NSGCYS- 5013.440Hydrophobic