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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:

2f59

2.300 Å

X-ray

2005-11-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:6,7-dimethyl-8-ribityllumazine synthase 1
ID:RISB1_BRUAB
AC:Q57DY1
Organism:Brucella abortus biovar 1
Reign:Bacteria
TaxID:262698
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A63 %
E37 %


Ligand binding site composition:

B-Factor:30.889
Number of residues:31
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.051489.375

% Hydrophobic% Polar
67.5932.41
According to VolSite

Ligand :
2f59_1 Structure
HET Code: INI
Formula: C9H14N4O8
Molecular weight: 306.229 g/mol
DrugBank ID: DB04162
Buried Surface Area:81.37 %
Polar Surface area: 196.96 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 7
Rings: 1
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 7

Mass center Coordinates

XYZ
98.283959.4756-91.6808


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
O2NALA- 532.66146.36H-Bond
(Protein Donor)
C8CD1LEU- 544.20Hydrophobic
C9CBLEU- 543.440Hydrophobic
O9NLEU- 542.9164.31H-Bond
(Protein Donor)
O10OE2GLU- 552.8136.71H-Bond
(Ligand Donor)
N3OTHR- 822.74160.59H-Bond
(Ligand Donor)
C8CG2VAL- 943.590Hydrophobic
O11OASN- 1152.9169.56H-Bond
(Ligand Donor)
C12CBASN- 1153.650Hydrophobic
O12NASN- 1152.95167.84H-Bond
(Protein Donor)
O11NZLYS- 1373.25176.79H-Bond
(Protein Donor)
C12CD2PHE- 1404.450Hydrophobic
C11CE2PHE- 1403.530Hydrophobic
C12CBALA- 1443.880Hydrophobic
O2OHOH- 3062.54179.97H-Bond
(Protein Donor)