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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:

1t13

2.900 Å

X-ray

2004-04-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:6,7-dimethyl-8-ribityllumazine synthase 2
ID:RISB2_BRUAB
AC:P61711
Organism:Brucella abortus biovar 1
Reign:Bacteria
TaxID:262698
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C31 %
D69 %


Ligand binding site composition:

B-Factor:39.069
Number of residues:32
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.081826.875

% Hydrophobic% Polar
50.6149.39
According to VolSite

Ligand :
1t13_4 Structure
HET Code: INI
Formula: C9H14N4O8
Molecular weight: 306.229 g/mol
DrugBank ID: DB04162
Buried Surface Area:64.37 %
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
68.16573.443915.9


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- 563142.23H-Bond
(Protein Donor)
O9NTYR- 572.75153.9H-Bond
(Protein Donor)
C10CBTYR- 573.90Hydrophobic
C9CBTYR- 573.240Hydrophobic
O10OE1GLU- 583.22125.71H-Bond
(Ligand Donor)
O12OE2GLU- 582.52123.67H-Bond
(Ligand Donor)
N3OPHE- 802.69170.96H-Bond
(Ligand Donor)
O4NILE- 822.82164.55H-Bond
(Protein Donor)
C8CG1VAL- 924.160Hydrophobic
C12CBLEU- 1123.70Hydrophobic
O11OSER- 1132.91160.13H-Bond
(Ligand Donor)
C12CBSER- 1134.360Hydrophobic
O12NSER- 1132.85158.1H-Bond
(Protein Donor)