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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:

2pmo

2.900 Å

X-ray

2007-04-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Protein kinase 7
ID:Q7YTF7_PLAF7
AC:Q7YTF7
Organism:Plasmodium falciparum
Reign:Eukaryota
TaxID:36329
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
X100 %


Ligand binding site composition:

B-Factor:32.062
Number of residues:24
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.847732.375

% Hydrophobic% Polar
49.7750.23
According to VolSite

Ligand :
2pmo_1 Structure
HET Code: HMD
Formula: C11H11BrN5O2
Molecular weight: 325.141 g/mol
DrugBank ID: DB02950
Buried Surface Area:67.24 %
Polar Surface area: 110.88 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 3
Rings: 3
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-11.8247-33.6469-18.0192


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
BR1CBLEU- 344.40Hydrophobic
C7CG2ILE- 423.850Hydrophobic
C7CBALA- 5340Hydrophobic
C7CD2LEU- 1013.770Hydrophobic
C7CD1TYR- 1173.830Hydrophobic
N2OGLU- 1182.96174.99H-Bond
(Ligand Donor)
O1NMET- 1202.73166.91H-Bond
(Protein Donor)
BR1CBASP- 1233.760Hydrophobic
C7CD1LEU- 1794.440Hydrophobic
N5OD2ASP- 1902.99163.9H-Bond
(Ligand Donor)