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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:

2q92

1.900 Å

X-ray

2007-06-12

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Methionine aminopeptidase
ID:MAP1_ECOLI
AC:P0AE18
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:18.138
Number of residues:30
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.609479.250

% Hydrophobic% Polar
40.1459.86
According to VolSite

Ligand :
2q92_1 Structure
HET Code: B23
Formula: C11H6NO5
Molecular weight: 232.169 g/mol
DrugBank ID: DB07408
Buried Surface Area:71.94 %
Polar Surface area: 99.09 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 0
Rings: 2
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-3.15806-0.07282359.08253


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
CAKCBTYR- 624.450Hydrophobic
CAICD2TYR- 623.480Hydrophobic
CAICBHIS- 633.810Hydrophobic
CAKCBTYR- 654.340Hydrophobic
OAONE2HIS- 1782.8141.22H-Bond
(Protein Donor)
OAMNE2HIS- 1783.23125.92H-Bond
(Protein Donor)
CAKCZ3TRP- 2213.390Hydrophobic
OANMN MN- 3002.330Metal Acceptor
OAOMN MN- 3002.230Metal Acceptor
OANMN MN- 3012.150Metal Acceptor