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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:

1rvv

2.400 Å

X-ray

1995-10-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:6,7-dimethyl-8-ribityllumazine synthase
ID:RISB_BACSU
AC:P11998
Organism:Bacillus subtilis
Reign:Bacteria
TaxID:224308
EC Number:2.5.1.78


Chains:

Chain Name:Percentage of Residues
within binding site
S4 %
U71 %
Y25 %


Ligand binding site composition:

B-Factor:18.760
Number of residues:28
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.3542176.875

% Hydrophobic% Polar
43.1056.90
According to VolSite

Ligand :
1rvv_25 Structure
HET Code: INI
Formula: C9H14N4O8
Molecular weight: 306.229 g/mol
DrugBank ID: DB04162
Buried Surface Area:65.56 %
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
-4.32824-8.5012454.0304


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- 562.89147.79H-Bond
(Protein Donor)
O9NPHE- 573.04170.91H-Bond
(Protein Donor)
C9CBPHE- 573.80Hydrophobic
O10OE1GLU- 582.85149.42H-Bond
(Ligand Donor)
N3OTHR- 802.86166.77H-Bond
(Ligand Donor)
C8CG2VAL- 924.320Hydrophobic
C12CG2ILE- 1123.640Hydrophobic
O11OPHE- 1133.28175.52H-Bond
(Ligand Donor)
C12CBPHE- 1133.580Hydrophobic
O12NPHE- 1133.21171.43H-Bond
(Protein Donor)