Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3cgt

2.400 Å

X-ray

1998-01-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Cyclomaltodextrin glucanotransferase
ID:CDGT1_BACCI
AC:P30920
Organism:Bacillus circulans
Reign:Bacteria
TaxID:1397
EC Number:2.4.1.19


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:22.175
Number of residues:38
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.415671.625

% Hydrophobic% Polar
42.2157.79
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3cgtHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
3cgt_1 Structure
HET Code: BCD
Formula: C42H70O35
Molecular weight: 1134.984 g/mol
DrugBank ID: DB03995
Buried Surface Area:39.33 %
Polar Surface area: 554.05 Å2
Number of
H-Bond Acceptors: 35
H-Bond Donors: 21
Rings: 9
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 7

Mass center Coordinates

XYZ
58.43511.94718.88791
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3cgtRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation802040Highcharts.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
C65CZTYR- 893.810Hydrophobic
C45CE2TYR- 894.140Hydrophobic
C24CD2TYR- 1003.850Hydrophobic
O64NE1TRP- 1012.72147.69H-Bond
(Protein Donor)
C15CZ2TRP- 1013.840Hydrophobic
C61CGPHE- 1833.650Hydrophobic
C62CE1PHE- 1834.240Hydrophobic
C67CE2PHE- 1834.180Hydrophobic
C62CD2LEU- 1944.270Hydrophobic
C63CD1LEU- 1943.880Hydrophobic
C63CE2TYR- 1954.50Hydrophobic
C64CD2TYR- 1954.330Hydrophobic
C66CD1TYR- 1953.730Hydrophobic
C67CE1TYR- 1953.680Hydrophobic
O65OD1ASP- 1963.13160.96H-Bond
(Ligand Donor)
C63CD1LEU- 1974.480Hydrophobic
C64CD1LEU- 1973.830Hydrophobic
O62NE2HIS- 2332.97159.54H-Bond
(Ligand Donor)
C22CD2PHE- 2593.930Hydrophobic
O23OD1ASP- 3283.14152.88H-Bond
(Ligand Donor)
O23OD2ASP- 3282.86142.81H-Bond
(Ligand Donor)
O33OD1ASP- 3282.53158.11H-Bond
(Ligand Donor)
O33OD2ASP- 3283.37129.28H-Bond
(Ligand Donor)
O34OD2ASP- 3712.9165.3H-Bond
(Ligand Donor)
O25OD2ASP- 3713.36147.97H-Bond
(Ligand Donor)
O24NH2ARG- 3752.95150.55H-Bond
(Protein Donor)
O24NH1ARG- 3753.39132.34H-Bond
(Protein Donor)
O25OHOH- 7533.25146.46H-Bond
(Protein Donor)
O33OHOH- 8222.74162.55H-Bond
(Protein Donor)
O24OHOH- 8702.77155.06H-Bond
(Protein Donor)