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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:

3myu

1.950 Å

X-ray

2010-05-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:High affinity transport system protein p37
ID:P37_MYCGE
AC:Q49410
Organism:Mycoplasma genitalium
Reign:Bacteria
TaxID:243273
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:35.356
Number of residues:29
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.395793.125

% Hydrophobic% Polar
27.6672.34
According to VolSite

Ligand :
3myu_1 Structure
HET Code: VIB
Formula: C12H17N4OS
Molecular weight: 265.355 g/mol
DrugBank ID: DB00152
Buried Surface Area:62.42 %
Polar Surface area: 104.15 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
4.0743330.708233.7392


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
N4AOD2ASP- 412.92154.1H-Bond
(Ligand Donor)
CM2CBASN- 1614.240Hydrophobic
CM4CD1TYR- 1764.110Hydrophobic
C7CZTYR- 1763.70Hydrophobic
C6CE2TYR- 1763.810Hydrophobic
CM4CBASP- 2694.140Hydrophobic
CM2CBTRP- 2753.740Hydrophobic
CM4CH2TRP- 2754.240Hydrophobic
DuArDuArTRP- 2753.970Aromatic Face/Face
CM4CZTYR- 3074.370Hydrophobic
C6CE1TYR- 3073.790Hydrophobic
S1CG1ILE- 3434.490Hydrophobic