Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3qvt

2.000 Å

X-ray

2011-02-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Myo-inositol-1-phosphate synthase (Ino1)
ID:O28480_ARCFU
AC:O28480
Organism:Archaeoglobus fulgidus
Reign:Archaea
TaxID:224325
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:23.990
Number of residues:59
Including
Standard Amino Acids: 56
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.315600.750

% Hydrophobic% Polar
43.8256.18
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3qvtHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
3qvt_1 Structure
HET Code: NAI
Formula: C21H27N7O14P2
Molecular weight: 663.425 g/mol
DrugBank ID: DB00157
Buried Surface Area:81.52 %
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
11.767126.281619.335
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3qvtRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation801020Highcharts.com


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
O1ANILE- 113.1153.06H-Bond
(Protein Donor)
O2NNVAL- 122.96172.56H-Bond
(Protein Donor)
C5DCG2VAL- 124.30Hydrophobic
O3BOE1GLU- 572.55174.69H-Bond
(Ligand Donor)
O2BOE2GLU- 572.72169.87H-Bond
(Ligand Donor)
O2BOE1GLU- 573.41127.17H-Bond
(Ligand Donor)
O3BNEARG- 593.18140.13H-Bond
(Protein Donor)
O3BNH2ARG- 592.88154.26H-Bond
(Protein Donor)
O2BNEARG- 593.14139.25H-Bond
(Protein Donor)
N6AOTHR- 992.86139.36H-Bond
(Ligand Donor)
C2BCD1LEU- 1103.80Hydrophobic
C5DCBVAL- 1474.490Hydrophobic
O3DOALA- 1482.71153.41H-Bond
(Ligand Donor)
O3DOG1THR- 1503.05156.81H-Bond
(Protein Donor)
N1AOHTYR- 1852.91130.3H-Bond
(Protein Donor)
C4NCE1PHE- 1994.360Hydrophobic
C4DCG2THR- 2004.150Hydrophobic
C1DCG2THR- 2004.410Hydrophobic
N7NOG1THR- 2282.97150.92H-Bond
(Ligand Donor)
C4NCG2THR- 2283.890Hydrophobic
O2DOD2ASP- 2613.14138.72H-Bond
(Ligand Donor)
N7NOASP- 3323.32138.11H-Bond
(Ligand Donor)