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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:

3i64

3.000 Å

X-ray

2009-07-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase
ID:NCSB1_STRCZ
AC:Q84HC8
Organism:Streptomyces carzinostaticus
Reign:Bacteria
TaxID:1897
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A96 %
B4 %


Ligand binding site composition:

B-Factor:63.972
Number of residues:22
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.687752.625

% Hydrophobic% Polar
52.4747.53
According to VolSite

Ligand :
3i64_1 Structure
HET Code: DNA
Formula: C11H7O4
Molecular weight: 203.171 g/mol
DrugBank ID: -
Buried Surface Area:71.57 %
Polar Surface area: 80.59 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-40.54132.2506-7.2572


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
C1HCG2VAL- 1034.050Hydrophobic
C1ISDMET- 1503.530Hydrophobic
C1MCEMET- 1503.660Hydrophobic
C1OCEMET- 1503.810Hydrophobic
O1COALA- 2433.43151.43H-Bond
(Ligand Donor)
C1ICBALA- 2434.50Hydrophobic
C1MSDMET- 2864.430Hydrophobic
C1HCDARG- 2893.710Hydrophobic
C1NCEMET- 2903.830Hydrophobic
C1OCEMET- 2903.790Hydrophobic
C1GCEMET- 2904.050Hydrophobic
C1FCE2TYR- 2933.40Hydrophobic
C1ECZPHE- 2943.370Hydrophobic