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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:

1x1b

2.600 Å

X-ray

2005-04-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:C-20 methyltransferase
ID:Q8KGE0_CHLTE
AC:Q8KGE0
Organism:Chlorobium tepidum
Reign:Bacteria
TaxID:194439
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:56.833
Number of residues:37
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.8271694.250

% Hydrophobic% Polar
56.5743.43
According to VolSite

Ligand :
1x1b_1 Structure
HET Code: SAH
Formula: C14H20N6O5S
Molecular weight: 384.411 g/mol
DrugBank ID: DB01752
Buried Surface Area:64.01 %
Polar Surface area: 212.38 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
39.472931.57275.81196


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
O3'OE1GLU- 1473.06158.33H-Bond
(Ligand Donor)
CBCBHIS- 1503.970Hydrophobic
NOGLY- 1773.25166.51H-Bond
(Ligand Donor)
O3'ND2ASN- 2003.39128.66H-Bond
(Protein Donor)
O2'OD1ASN- 2002.99168.77H-Bond
(Ligand Donor)
C2'CD1LEU- 2014.060Hydrophobic
C1'CGLEU- 2014.430Hydrophobic
N6OD1ASP- 2272.62154.93H-Bond
(Ligand Donor)
N1NILE- 2283.12165.85H-Bond
(Protein Donor)
NOCYS- 2422.84157.38H-Bond
(Ligand Donor)
OCZARG- 2433.680Ionic
(Protein Cationic)
OXTCZARG- 2433.150Ionic
(Protein Cationic)
ONEARG- 2432.69154.66H-Bond
(Protein Donor)
OXTNH2ARG- 2432.57144.42H-Bond
(Protein Donor)
OXTNEARG- 2432.96132.56H-Bond
(Protein Donor)