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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:

5ahw

2.150 Å

X-ray

2015-02-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Universal stress protein family protein, putative
ID:A0QYW6_MYCS2
AC:A0QYW6
Organism:Mycobacterium smegmatis 155)
Reign:Bacteria
TaxID:246196
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:41.922
Number of residues:32
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.517324.000

% Hydrophobic% Polar
54.1745.83
According to VolSite

Ligand :
5ahw_5 Structure
HET Code: CMP
Formula: C10H11N5O6P
Molecular weight: 328.198 g/mol
DrugBank ID: DB02527
Buried Surface Area:76.63 %
Polar Surface area: 167.48 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 2
Rings: 4
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 1

Mass center Coordinates

XYZ
16.489437.274452.8676


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
O2'OGLY- 102.53161.69H-Bond
(Ligand Donor)
O2POGSER- 162.67150.38H-Bond
(Ligand Donor)
C3'CBSER- 173.880Hydrophobic
N6OALA- 402.9167.28H-Bond
(Ligand Donor)
N1NALA- 402.94173.46H-Bond
(Protein Donor)
C4'CBVAL- 1134.430Hydrophobic
C1'CG1VAL- 1134.390Hydrophobic
O2'NGLY- 1143.44154.15H-Bond
(Protein Donor)
O5'NVAL- 1163.05145.08H-Bond
(Protein Donor)
C5'CBVAL- 1163.790Hydrophobic
C1'CG1VAL- 1293.70Hydrophobic
C5'CGPRO- 1304.240Hydrophobic
O1POG1THR- 1462.6164.68H-Bond
(Protein Donor)