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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:

1qmf

2.800 Å

X-ray

1999-09-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Penicillin-binding protein 2x
ID:PBPX_STRPN
AC:P14677
Organism:Streptococcus pneumoniae serotype 4
Reign:Bacteria
TaxID:170187
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:48.298
Number of residues:28
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1831063.125

% Hydrophobic% Polar
44.1355.87
According to VolSite

Ligand :
1qmf_1 Structure
HET Code: KEF
Formula: C16H15N4O8S
Molecular weight: 423.377 g/mol
DrugBank ID: -
Buried Surface Area:40.91 %
Polar Surface area: 201.89 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 2
Rings: 3
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 8

Mass center Coordinates

XYZ
103.8161.888749.4971


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
C2CG1VAL- 4233.760Hydrophobic
N31OPRO- 4243.13126.43H-Bond
(Ligand Donor)
O4ANH2ARG- 4263.07150.86H-Bond
(Protein Donor)
O4BNEARG- 4262.74160.05H-Bond
(Protein Donor)
O4ACZARG- 4263.810Ionic
(Protein Cationic)
O4BCZARG- 4263.580Ionic
(Protein Cationic)
C3'CG1VAL- 6623.950Hydrophobic
S1CG2THR- 6654.240Hydrophobic
N31OHOH- 20572.88121.86H-Bond
(Ligand Donor)