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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:

1sb9

2.500 Å

X-ray

2004-02-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:WbpP
ID:Q8KN66_PSEAI
AC:Q8KN66
Organism:Pseudomonas aeruginosa
Reign:Bacteria
TaxID:287
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:32.957
Number of residues:47
Including
Standard Amino Acids: 41
Non Standard Amino Acids: 1
Water Molecules: 5
Cofactors: NAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0041269.000

% Hydrophobic% Polar
39.1060.90
According to VolSite

Ligand :
1sb9_1 Structure
HET Code: UPG
Formula: C15H22N2O17P2
Molecular weight: 564.286 g/mol
DrugBank ID: DB01861
Buried Surface Area:63.66 %
Polar Surface area: 316.82 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 7
Rings: 3
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 9

Mass center Coordinates

XYZ
40.4237.4976491.4081


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
O4'NSER- 1033.42160.63H-Bond
(Protein Donor)
C6'CBSER- 1424.230Hydrophobic
O6'OGSER- 1422.64140.21H-Bond
(Protein Donor)
C6'CBSER- 1444.030Hydrophobic
C6'CE2TYR- 1663.460Hydrophobic
O2BND2ASN- 1953.18138.87H-Bond
(Protein Donor)
C1CCG2VAL- 2104.360Hydrophobic
C4CCBVAL- 2104.420Hydrophobic
C5CCG1VAL- 2103.880Hydrophobic
O2ANVAL- 2103171.25H-Bond
(Protein Donor)
O4NE1TRP- 2143.43132.25H-Bond
(Protein Donor)
N3OTYR- 2252.64162.72H-Bond
(Ligand Donor)
O2NASN- 2272.77171.66H-Bond
(Protein Donor)
O2CND2ASN- 2273.07162.35H-Bond
(Protein Donor)
O2BNEARG- 2343.27152.56H-Bond
(Protein Donor)
C1CCD1LEU- 2713.870Hydrophobic
C4CCD2LEU- 2713.980Hydrophobic
O1ANH2ARG- 2992.83156.48H-Bond
(Protein Donor)
O1BNH2ARG- 2993.34124.93H-Bond
(Protein Donor)
O1ACZARG- 2993.840Ionic
(Protein Cationic)
O3COD1ASP- 3022.97142.89H-Bond
(Ligand Donor)
O3COD2ASP- 3022.79148.51H-Bond
(Ligand Donor)
C2'C4NNAD- 3424.380Hydrophobic
C3'C3NNAD- 3424.350Hydrophobic
C6'C5NNAD- 3424.060Hydrophobic
C4'C4NNAD- 3423.690Hydrophobic
O1AOHOH- 3742.63159.05H-Bond
(Protein Donor)
O2COHOH- 3852.87164.74H-Bond
(Protein Donor)