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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:

3kds

2.600 Å

X-ray

2009-10-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:ATP-dependent zinc metalloprotease FtsH
ID:FTSH_THEMA
AC:Q9WZ49
Organism:Thermotoga maritima
Reign:Bacteria
TaxID:243274
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
G100 %


Ligand binding site composition:

B-Factor:78.635
Number of residues:28
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.804894.375

% Hydrophobic% Polar
43.0256.98
According to VolSite

Ligand :
3kds_3 Structure
HET Code: NHX
Formula: C24H32N4O5
Molecular weight: 456.535 g/mol
DrugBank ID: -
Buried Surface Area:42.75 %
Polar Surface area: 150.61 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 5
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 11

Mass center Coordinates

XYZ
33.0879114.0150.7821


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
CAACG2ILE- 4203.620Hydrophobic
CAACBHIS- 4234.390Hydrophobic
OAIOE2GLU- 4242.66177.92H-Bond
(Protein Donor)
NOLYS- 4513.35150.41H-Bond
(Ligand Donor)
CBCBLYS- 4513.720Hydrophobic
CANCBALA- 4523.710Hydrophobic
CBCCBALA- 4524.230Hydrophobic
CBCD1LEU- 4534.080Hydrophobic
CBDCBLEU- 4534.20Hydrophobic
OAGNLEU- 4532.89154.96H-Bond
(Protein Donor)
NATOGLY- 4543.29176.6H-Bond
(Ligand Donor)
CAOCBASN- 4993.590Hydrophobic
OAFZN ZN- 9962.110Metal Acceptor
OAIZN ZN- 9962.130Metal Acceptor