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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:

3l7g

2.700 Å

X-ray

2009-12-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Xaa-Pro dipeptidase
ID:PEPQ_ALTSX
AC:Q44238
Organism:Alteromonas sp
Reign:Bacteria
TaxID:232
EC Number:3.4.13.9


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:29.038
Number of residues:21
Including
Standard Amino Acids: 19
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.293418.500

% Hydrophobic% Polar
45.1654.84
According to VolSite

Ligand :
3l7g_2 Structure
HET Code: M44
Formula: C6H16N2O2P
Molecular weight: 179.177 g/mol
DrugBank ID: -
Buried Surface Area:59.69 %
Polar Surface area: 74 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 2
Rings: 0
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
32.39372.788934.2521


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
C2CE2TYR- 2123.660Hydrophobic
C3CD2TYR- 2124.240Hydrophobic
C3CD1ILE- 2154.020Hydrophobic
C6CBHIS- 3323.810Hydrophobic
C2CG1VAL- 3423.790Hydrophobic
O2NE2HIS- 3433162.68H-Bond
(Protein Donor)
N2OE1GLU- 3812.54138.17H-Bond
(Ligand Donor)
O1MN MN- 5191.840Metal Acceptor
O1MN MN- 5202.240Metal Acceptor