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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:

4zas

2.470 Å

X-ray

2015-04-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:CalS13
ID:Q8KND8_MICEC
AC:Q8KND8
Organism:Micromonospora echinospora
Reign:Bacteria
TaxID:1877
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
E50 %
F50 %


Ligand binding site composition:

B-Factor:67.629
Number of residues:22
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9861042.875

% Hydrophobic% Polar
52.1047.90
According to VolSite

Ligand :
4zas_2 Structure
HET Code: TYD
Formula: C10H13N2O11P2
Molecular weight: 399.165 g/mol
DrugBank ID: DB03103
Buried Surface Area:47.23 %
Polar Surface area: 220.27 Å2
Number of
H-Bond Acceptors: 11
H-Bond Donors: 2
Rings: 2
Aromatic rings: 0
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
14.683249.2929.4871


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
C4'CBSER- 134.390Hydrophobic
N3OGLY- 322.64150.11H-Bond
(Ligand Donor)
O4NLEU- 342.7150.75H-Bond
(Protein Donor)
O4NGLU- 353.19170.44H-Bond
(Protein Donor)
C5MCBGLU- 354.120Hydrophobic
C5MCBALA- 2004.220Hydrophobic
C1'CG2ILE- 2014.270Hydrophobic
C5'CD1ILE- 2013.90Hydrophobic
O1ACZARG- 2373.920Ionic
(Protein Cationic)
O1ANH1ARG- 2372.85128.66H-Bond
(Protein Donor)