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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:

2gl0

2.250 Å

X-ray

2006-04-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:Q8ZVF7_PYRAE
AC:Q8ZVF7
Organism:Pyrobaculum aerophilum
Reign:Archaea
TaxID:178306
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D68 %
F32 %


Ligand binding site composition:

B-Factor:15.067
Number of residues:24
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.418465.750

% Hydrophobic% Polar
47.1052.90
According to VolSite

Ligand :
2gl0_6 Structure
HET Code: ADN
Formula: C10H13N5O4
Molecular weight: 267.241 g/mol
DrugBank ID: DB00640
Buried Surface Area:64.35 %
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
-15.1536-14.37683.08237


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
O2'OD1ASN- 202.58169.61H-Bond
(Ligand Donor)
C4'CBPHE- 284.470Hydrophobic
C1'CBPHE- 283.980Hydrophobic
DuArDuArPHE- 283.750Aromatic Face/Face
DuArDuArTRP- 953.50Aromatic Face/Face
C2'CZ3TRP- 954.280Hydrophobic
O3'NALA- 1172.62151.33H-Bond
(Protein Donor)
C3'CBALA- 1174.290Hydrophobic
N1OHTYR- 1652.6165.87H-Bond
(Protein Donor)
N3OHOH- 9092.83179.99H-Bond
(Protein Donor)