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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:

3pm1

2.800 Å

X-ray

2010-11-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:HTH-type transcriptional regulator QacR
ID:QACR_STAAM
AC:P0A0N3
Organism:Staphylococcus aureus
Reign:Bacteria
TaxID:158878
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A96 %
B4 %


Ligand binding site composition:

B-Factor:59.233
Number of residues:24
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.407931.500

% Hydrophobic% Polar
54.7145.29
According to VolSite

Ligand :
3pm1_1 Structure
HET Code: ET
Formula: C21H20N3
Molecular weight: 314.404 g/mol
DrugBank ID: -
Buried Surface Area:57.43 %
Polar Surface area: 55.92 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 2
Rings: 4
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
36.9108-9.811839.35904


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
C2CBSER- 863.890Hydrophobic
C3CGGLN- 903.960Hydrophobic
C17CG2ILE- 994.450Hydrophobic
C22CD1ILE- 994.30Hydrophobic
C18SDMET- 1164.470Hydrophobic
C19CD2LEU- 1194.430Hydrophobic
C7CGGLU- 1204.450Hydrophobic
C19CGGLU- 1203.570Hydrophobic
C12CBTYR- 1233.940Hydrophobic
C9CBALA- 1534.30Hydrophobic
N24OD1ASN- 1543.44132.01H-Bond
(Ligand Donor)
C9CBASN- 15740Hydrophobic