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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:

3a8i

1.990 Å

X-ray

2009-10-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aminomethyltransferase
ID:GCST_ECOLI
AC:P27248
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:2.1.2.10


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:18.909
Number of residues:33
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.004786.375

% Hydrophobic% Polar
54.5145.49
According to VolSite

Ligand :
3a8i_3 Structure
HET Code: C2F
Formula: C20H23N7O6
Molecular weight: 457.440 g/mol
DrugBank ID: -
Buried Surface Area:59.47 %
Polar Surface area: 204.14 Å2
Number of
H-Bond Acceptors: 11
H-Bond Donors: 5
Rings: 3
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 9

Mass center Coordinates

XYZ
7.5094513.544741.517


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
C11SDMET- 513.760Hydrophobic
C9CE1TYR- 843.940Hydrophobic
C15CE1TYR- 843.290Hydrophobic
N10OD2ASP- 973.01122.63H-Bond
(Ligand Donor)
C17CD1ILE- 993.740Hydrophobic
N8OVAL- 1112.99163.81H-Bond
(Ligand Donor)
CBCZPHE- 1734.30Hydrophobic
C11CE1TYR- 1884.140Hydrophobic
NA2OE1GLU- 1952.62159.44H-Bond
(Ligand Donor)
N3OE2GLU- 1952.83149.38H-Bond
(Ligand Donor)
N3OE1GLU- 1953.06132.09H-Bond
(Ligand Donor)
C12SDMET- 2324.190Hydrophobic
C13CBMET- 2323.680Hydrophobic
CBCH2TRP- 2523.50Hydrophobic
O4OHOH- 6692.61179.98H-Bond
(Protein Donor)