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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:

3iu7

1.400 Å

X-ray

2009-08-30

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Methionine aminopeptidase 2
ID:MAP12_MYCTU
AC:P9WK19
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:7.862
Number of residues:23
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.675519.750

% Hydrophobic% Polar
49.3550.65
According to VolSite

Ligand :
3iu7_1 Structure
HET Code: FCD
Formula: C11H6ClO3
Molecular weight: 221.617 g/mol
DrugBank ID: DB02909
Buried Surface Area:64.46 %
Polar Surface area: 53.27 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 0
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-35.2806-29.7845-5.5202


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
CL2CG2THR- 943.990Hydrophobic
CL2CD2TYR- 974.070Hydrophobic
C5CD2TYR- 973.470Hydrophobic
C4CDLYS- 984.150Hydrophobic
CL2CGPHE- 1003.830Hydrophobic
CL2SGCYS- 1054.190Hydrophobic
OANE2HIS- 2123.34121.46H-Bond
(Protein Donor)
OBNE2HIS- 2122.69165.88H-Bond
(Protein Donor)
C5CZ3TRP- 2553.450Hydrophobic
OXTMN MN- 2862.140Metal Acceptor
OBMN MN- 2872.410Metal Acceptor
OXTMN MN- 2872.220Metal Acceptor