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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:

3gxo

2.300 Å

X-ray

2009-04-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Mitomycin biosynthesis 6-O-methyltransferase
ID:MMCR_STRLA
AC:Q9X5T6
Organism:Streptomyces lavendulae
Reign:Bacteria
TaxID:1914
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C9 %
D91 %


Ligand binding site composition:

B-Factor:35.617
Number of residues:34
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.409941.625

% Hydrophobic% Polar
54.8445.16
According to VolSite

Ligand :
3gxo_4 Structure
HET Code: MQA
Formula: C16H20N3O6
Molecular weight: 350.346 g/mol
DrugBank ID: -
Buried Surface Area:66.24 %
Polar Surface area: 124.77 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 2
Rings: 4
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
33.03884.4108448.195


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
C3CE2PHE- 1133.80Hydrophobic
CM6CE2PHE- 1454.190Hydrophobic
CM6CE1PHE- 1593.590Hydrophobic
C3CBALA- 1624.460Hydrophobic
N2OALA- 1623.21152.08H-Bond
(Ligand Donor)
C10SDMET- 1633.930Hydrophobic
C24SDMET- 1633.930Hydrophobic
C10CG2VAL- 1664.170Hydrophobic
C24CBHIS- 2564.230Hydrophobic
O7OD1ASP- 2602.82154.34H-Bond
(Protein Donor)
C25CG2VAL- 3013.740Hydrophobic
CM6CD1LEU- 3084.230Hydrophobic