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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:

5ckw

2.490 Å

X-ray

2015-07-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:Q5WZW9_LEGPL
AC:Q5WZW9
Organism:Legionella pneumophila
Reign:Bacteria
TaxID:297245
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:90.694
Number of residues:33
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: MG MG

Cavity properties

LigandabilityVolume (Å3)
0.467749.250

% Hydrophobic% Polar
49.1050.90
According to VolSite

Ligand :
5ckw_1 Structure
HET Code: ANP
Formula: C10H13N6O12P3
Molecular weight: 502.164 g/mol
DrugBank ID: -
Buried Surface Area:55.05 %
Polar Surface area: 322.68 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-34.0141-31.34499.87474


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
C1'CG2ILE- 794.030Hydrophobic
C4'CG2ILE- 793.380Hydrophobic
C5'CGGLN- 894.170Hydrophobic
C4'CZPHE- 1024.40Hydrophobic
C1'CE1PHE- 1023.640Hydrophobic
DuArDuArPHE- 1023.950Aromatic Face/Face
O1BNZLYS- 1043.38150.99H-Bond
(Protein Donor)
O2ANZLYS- 1042.84154.41H-Bond
(Protein Donor)
O1BNZLYS- 1043.380Ionic
(Protein Cationic)
O1ANZLYS- 1043.760Ionic
(Protein Cationic)
O2ANZLYS- 1042.840Ionic
(Protein Cationic)
N6OTHR- 1462.85138.45H-Bond
(Ligand Donor)
N1NILE- 1482.7165.7H-Bond
(Protein Donor)
O2'SDMET- 2022.76158.84Weak HBond LIG
C2'SDMET- 2023.770Hydrophobic
C2'CG2VAL- 2124.480Hydrophobic
O2BMG MG- 5022.020Metal Acceptor
O3AMG MG- 5022.760Metal Acceptor