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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:

3qgz

1.100 Å

X-ray

2011-01-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Histidine triad nucleotide-binding protein 1
ID:HINT1_RABIT
AC:P80912
Organism:Oryctolagus cuniculus
Reign:Eukaryota
TaxID:9986
EC Number:3


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:14.517
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.629327.375

% Hydrophobic% Polar
61.8638.14
According to VolSite

Ligand :
3qgz_1 Structure
HET Code: ADN
Formula: C10H13N5O4
Molecular weight: 267.241 g/mol
DrugBank ID: DB00640
Buried Surface Area:55.25 %
Polar Surface area: 139.54 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
8.2436810.628155.3425


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
C1'CZPHE- 194.370Hydrophobic
C5'CZPHE- 193.980Hydrophobic
O3'OD2ASP- 432.58163.5H-Bond
(Ligand Donor)
O2'OD1ASP- 432.83169.86H-Bond
(Ligand Donor)
N3NILE- 443.21153.76H-Bond
(Protein Donor)
C2'CG2ILE- 444.180Hydrophobic
C4'CD1LEU- 5340Hydrophobic
C1'CD1LEU- 534.070Hydrophobic
C5'CG2VAL- 1084.210Hydrophobic
O5'NE2HIS- 1122.52136.36H-Bond
(Ligand Donor)