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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:

3pmu

1.430 Å

X-ray

2010-11-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Endothiapepsin
ID:CARP_CRYPA
AC:P11838
Organism:Cryphonectria parasitica
Reign:Eukaryota
TaxID:5116
EC Number:3.4.23.22


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:15.990
Number of residues:21
Including
Standard Amino Acids: 18
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.323425.250

% Hydrophobic% Polar
39.6860.32
According to VolSite

Ligand :
3pmu_1 Structure
HET Code: F7L
Formula: C14H21FNO2
Molecular weight: 254.320 g/mol
DrugBank ID: -
Buried Surface Area:50.06 %
Polar Surface area: 33.9 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 2
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-2.633286.220728.12078


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
C17CD2TYR- 793.460Hydrophobic
C3CBASP- 814.250Hydrophobic
C9CBASP- 814.090Hydrophobic
C17CD2LEU- 1253.50Hydrophobic
N14OGLY- 2212.96132.64H-Bond
(Ligand Donor)
C5CG2THR- 2224.150Hydrophobic
C3CBTHR- 2224.060Hydrophobic
C5CE2TYR- 2264.430Hydrophobic
F12CG2ILE- 3003.750Hydrophobic
C11CD1ILE- 3004.170Hydrophobic
C5CD1ILE- 3043.260Hydrophobic