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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:

1jhr

2.000 Å

X-ray

2001-06-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
ID:COBT_SALTY
AC:Q05603
Organism:Salmonella typhimurium
Reign:Bacteria
TaxID:99287
EC Number:2.4.2.21


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:17.635
Number of residues:35
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.939455.625

% Hydrophobic% Polar
51.1148.89
According to VolSite

Ligand :
1jhr_2 Structure
HET Code: P2P
Formula: C10H11N4O8P
Molecular weight: 346.190 g/mol
DrugBank ID: DB02905
Buried Surface Area:66.18 %
Polar Surface area: 195.75 Å2
Number of
H-Bond Acceptors: 11
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 4

Mass center Coordinates

XYZ
57.927940.426810.568


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
N3NE2GLN- 883.04161.43H-Bond
(Protein Donor)
O2'OE1GLU- 1742.57155.61H-Bond
(Ligand Donor)
O3'NGLY- 1762.82167.29H-Bond
(Protein Donor)
O3PNALA- 1782.72160.47H-Bond
(Protein Donor)
O1PNTHR- 1803.04155.47H-Bond
(Protein Donor)
O1POG1THR- 1802.66163.67H-Bond
(Protein Donor)
C5'CG2THR- 1803.230Hydrophobic
O2PNALA- 2032.85173.23H-Bond
(Protein Donor)
O6'NALA- 2033.38122.12H-Bond
(Protein Donor)
O2POHOH- 10402.63170.95H-Bond
(Protein Donor)