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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:

3nt4

2.500 Å

X-ray

2010-07-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
ID:IOLG_BACSU
AC:P26935
Organism:Bacillus subtilis
Reign:Bacteria
TaxID:224308
EC Number:1.1.1.18


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:70.367
Number of residues:41
Including
Standard Amino Acids: 37
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.240644.625

% Hydrophobic% Polar
40.3159.69
According to VolSite

Ligand :
3nt4_1 Structure
HET Code: NAI
Formula: C21H27N7O14P2
Molecular weight: 663.425 g/mol
DrugBank ID: DB00157
Buried Surface Area:53.36 %
Polar Surface area: 342.9 Å2
Number of
H-Bond Acceptors: 19
H-Bond Donors: 6
Rings: 5
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
-58.2857-12.653220.2792


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
O2ANALA- 123.26172.81H-Bond
(Protein Donor)
O2NNILE- 132.79160.95H-Bond
(Protein Donor)
C5DCG2ILE- 133.620Hydrophobic
C4NCG1ILE- 134.260Hydrophobic
O3BOD2ASP- 353.33173.82H-Bond
(Ligand Donor)
O3BOD1ASP- 353.48135.12H-Bond
(Ligand Donor)
O2BOD2ASP- 352.82153.88H-Bond
(Ligand Donor)
O2BOD1ASP- 353.4138.86H-Bond
(Ligand Donor)
N3ANVAL- 363.18143.65H-Bond
(Protein Donor)
C1BCBVAL- 364.390Hydrophobic
C1BCBSER- 744.380Hydrophobic
C1DCBGLU- 964.30Hydrophobic
N7NOHTYR- 2802.97139.71H-Bond
(Ligand Donor)
O2NOHOH- 3472.56179.96H-Bond
(Protein Donor)