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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:

2evm

1.700 Å

X-ray

2005-10-31

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:13.848
Number of residues:28
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.642462.375

% Hydrophobic% Polar
46.7253.28
According to VolSite

Ligand :
2evm_1 Structure
HET Code: FC2
Formula: C11H5Cl2O3
Molecular weight: 256.062 g/mol
DrugBank ID: DB07758
Buried Surface Area:65.17 %
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
-3.021-1.00258.51931


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
CL1CBCYS- 594.230Hydrophobic
CL2CE2TYR- 624.320Hydrophobic
C4CBHIS- 633.490Hydrophobic
C3CBTYR- 654.350Hydrophobic
CL1CGTYR- 653.50Hydrophobic
CL1SGCYS- 703.970Hydrophobic
OANE2HIS- 1783.34123.17H-Bond
(Protein Donor)
OBNE2HIS- 1782.74156.21H-Bond
(Protein Donor)
C3CZ3TRP- 2213.430Hydrophobic
OXTMN MN- 9012.10Metal Acceptor
OBMN MN- 9022.240Metal Acceptor
OXTMN MN- 9022.320Metal Acceptor