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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:

2gg3

1.450 Å

X-ray

2006-03-23

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:15.726
Number of residues:24
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.450391.500

% Hydrophobic% Polar
48.2851.72
According to VolSite

Ligand :
2gg3_1 Structure
HET Code: U13
Formula: C9H9FN6
Molecular weight: 220.206 g/mol
DrugBank ID: DB08667
Buried Surface Area:64.69 %
Polar Surface area: 102.67 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 2
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-3.21406-0.4185638.81312


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
F7CE2TYR- 624.110Hydrophobic
C1CD2TYR- 623.380Hydrophobic
F7CBHIS- 633.370Hydrophobic
C1CBTYR- 654.370Hydrophobic
N16OD1ASP- 973.35143.11H-Bond
(Ligand Donor)
N18NE2HIS- 1713.42124.08H-Bond
(Ligand Donor)
N17OE2GLU- 2043.4152.31H-Bond
(Ligand Donor)
F7CH2TRP- 2213.430Hydrophobic