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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:

2qim

1.350 Å

X-ray

2007-07-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Class 10 plant pathogenesis-related protein
ID:Q9LLQ2_LUPLU
AC:Q9LLQ2
Organism:Lupinus luteus
Reign:Eukaryota
TaxID:3873
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:18.473
Number of residues:24
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1551495.125

% Hydrophobic% Polar
56.2143.79
According to VolSite

Ligand :
2qim_3 Structure
HET Code: ZEA
Formula: C10H13N5O
Molecular weight: 219.243 g/mol
DrugBank ID: DB11337
Buried Surface Area:53.72 %
Polar Surface area: 86.72 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
60.579144.01744.564


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
C11CD1ILE- 374.110Hydrophobic
C15CD2LEU- 554.310Hydrophobic
C11CD2LEU- 553.970Hydrophobic
DuArDuArPHE- 573.60Aromatic Face/Face
N7OE2GLU- 592.71172.32H-Bond
(Ligand Donor)
C14CGPHE- 1423.940Hydrophobic
C15CE1PHE- 1424.050Hydrophobic
O16OHOH- 1732.93179.96H-Bond
(Protein Donor)