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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:

1ldq

2.700 Å

X-ray

2002-04-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Avidin
ID:AVID_CHICK
AC:P02701
Organism:Gallus gallus
Reign:Eukaryota
TaxID:9031
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:33.877
Number of residues:21
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.817253.125

% Hydrophobic% Polar
66.6733.33
According to VolSite

Ligand :
1ldq_1 Structure
HET Code: SHM
Formula: C11H17N2O3S
Molecular weight: 257.329 g/mol
DrugBank ID: DB03112
Buried Surface Area:45.72 %
Polar Surface area: 106.55 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 2
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-1.77329.336725.0629


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
O17OHTYR- 332.86157.86H-Bond
(Protein Donor)
C10CZ2TRP- 703.40Hydrophobic
S7CZ2TRP- 703.520Hydrophobic
C10CZPHE- 724.450Hydrophobic
C12CE2PHE- 7240Hydrophobic
S7CG2THR- 773.720Hydrophobic
C8CE2TRP- 973.420Hydrophobic
C11CD2LEU- 993.930Hydrophobic
C6CD2LEU- 994.310Hydrophobic
N5OD1ASN- 1183.13145.15H-Bond
(Ligand Donor)