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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:

5bz4

2.430 Å

X-ray

2015-06-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Beta-ketothiolase
ID:A0QUH3_MYCS2
AC:A0QUH3
Organism:Mycobacterium smegmatis 155)
Reign:Bacteria
TaxID:246196
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
K95 %
L5 %


Ligand binding site composition:

B-Factor:39.936
Number of residues:41
Including
Standard Amino Acids: 38
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.606860.625

% Hydrophobic% Polar
39.6160.39
According to VolSite

Ligand :
5bz4_5 Structure
HET Code: COA
Formula: C21H32N7O16P3S
Molecular weight: 763.502 g/mol
DrugBank ID: DB01992
Buried Surface Area:43.48 %
Polar Surface area: 426.11 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 6
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 18

Mass center Coordinates

XYZ
64.6857-93.976242.8255


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
S1PSGCYS- 903.310Hydrophobic
O1ACZARG- 1363.010Ionic
(Protein Cationic)
S1PSDMET- 1633.980Hydrophobic
CAPCD1LEU- 1644.340Hydrophobic
DuArCZARG- 2263.7324.08Pi/Cation
C1BCD2LEU- 2374.060Hydrophobic
CEPCBALA- 2523.520Hydrophobic
C5BCBALA- 2523.560Hydrophobic
N8POSER- 2563.19124.58H-Bond
(Ligand Donor)
CDPCBGLN- 2584.180Hydrophobic
C6PCGGLN- 2583.990Hydrophobic
O9PNE2GLN- 2582.96123H-Bond
(Protein Donor)
S1PSDMET- 2973.850Hydrophobic
C2PCBALA- 3273.50Hydrophobic
C2PCZPHE- 3284.220Hydrophobic
S1PSGCYS- 3904.260Hydrophobic
N4POHOH- 6273.13157.9H-Bond
(Ligand Donor)
N1AOHOH- 6522.9161.14H-Bond
(Protein Donor)