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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:

4i9b

1.900 Å

X-ray

2012-12-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Putative betaine aldehyde dehyrogenase
ID:Q56R04_SOLLC
AC:Q56R04
Organism:Solanum lycopersicum
Reign:Eukaryota
TaxID:4081
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:23.230
Number of residues:34
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.548624.375

% Hydrophobic% Polar
39.4660.54
According to VolSite

Ligand :
4i9b_2 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:60.33 %
Polar Surface area: 343.54 Å2
Number of
H-Bond Acceptors: 18
H-Bond Donors: 6
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
-7.26613.2123-26.8661


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
C1BCG2ILE- 1583.580Hydrophobic
C4BCG2ILE- 1583.630Hydrophobic
O3BOTHR- 1592.83163.03H-Bond
(Ligand Donor)
O1NNE1TRP- 1612.85144.81H-Bond
(Protein Donor)
O5DNE1TRP- 1613.33132.97H-Bond
(Protein Donor)
O2BNZLYS- 1852.76171.97H-Bond
(Protein Donor)
C3BCBSER- 1874.070Hydrophobic
O2BOE2GLU- 1882.59142.97H-Bond
(Ligand Donor)
C5BCE1PHE- 2363.770Hydrophobic
O2AOGSER- 2392.84154.05H-Bond
(Protein Donor)
O2ANSER- 2392.51167.99H-Bond
(Protein Donor)
O1AOG1THR- 2422.92164H-Bond
(Protein Donor)
O2AOG1THR- 2423.44120.39H-Bond
(Protein Donor)
C1BCG2THR- 2424.270Hydrophobic