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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:

3dh8

1.800 Å

X-ray

2008-06-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein PA1000
ID:Y1000_PSEAE
AC:P20581
Organism:Pseudomonas aeruginosa
Reign:Bacteria
TaxID:208964
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:35.225
Number of residues:31
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: FE FE

Cavity properties

LigandabilityVolume (Å3)
1.060513.000

% Hydrophobic% Polar
65.7934.21
According to VolSite

Ligand :
3dh8_1 Structure
HET Code: B4N
Formula: C12H8N2O8P
Molecular weight: 339.174 g/mol
DrugBank ID: DB07418
Buried Surface Area:73.14 %
Polar Surface area: 160.03 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 0
Rings: 2
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 2
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-17.51152.33339-11.2094


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
CAMCBHIS- 713.970Hydrophobic
CALCBALA- 1824.50Hydrophobic
CAKCBALA- 1823.570Hydrophobic
OAACZARG- 1913.820Ionic
(Protein Cationic)
OAANH1ARG- 1912.8157.82H-Bond
(Protein Donor)
CAHCD2LEU- 1933.410Hydrophobic
CAGCD1LEU- 1933.650Hydrophobic
OADNE2GLN- 2723.17134.56H-Bond
(Protein Donor)
CAKCBSER- 2734.310Hydrophobic
CALCBSER- 2734.340Hydrophobic
CAJCD2LEU- 2774.410Hydrophobic
CAQCD1LEU- 2774.090Hydrophobic
CAHCD2LEU- 2773.730Hydrophobic
CAMCD2LEU- 2814.360Hydrophobic
CANCD2LEU- 2814.060Hydrophobic
CAJCBSER- 2854.330Hydrophobic
OAENH1ARG- 2883.45175.91H-Bond
(Protein Donor)
OACFE FE- 9982.470Metal Acceptor
OAFFE FE- 9992.030Metal Acceptor