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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:

2q14

2.200 Å

X-ray

2007-05-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Phosphohydrolase
ID:Q8A013_BACTN
AC:Q8A013
Organism:Bacteroides thetaiotaomicron
Reign:Bacteria
TaxID:226186
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A4 %
C46 %
D50 %


Ligand binding site composition:

B-Factor:32.923
Number of residues:27
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.113941.625

% Hydrophobic% Polar
28.6771.33
According to VolSite

Ligand :
2q14_4 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:44.27 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-35.8777-22.9705-54.3503


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'OILE- 72.55163.54H-Bond
(Ligand Donor)
N7OHTYR- 242.79164.12H-Bond
(Protein Donor)
N6OE1GLN- 333.31152.86H-Bond
(Ligand Donor)
C4'CG1VAL- 474.050Hydrophobic
O3BNZLYS- 2023.890Ionic
(Protein Cationic)
O2AOG1THR- 2263.14145.18H-Bond
(Protein Donor)
C5'CBTHR- 2263.940Hydrophobic
O1ANH1ARG- 3133.25171.86H-Bond
(Protein Donor)
O5'NH2ARG- 3133.37160.43H-Bond
(Protein Donor)
DuArCZARG- 3133.6518.85Pi/Cation
O2'OHOH- 5343.42180H-Bond
(Protein Donor)