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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:

3jqp

3.000 Å

X-ray

2009-09-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Ferredoxin--NADP reductase, apicoplast
ID:C6KT68_PLAF7
AC:C6KT68
Organism:Plasmodium falciparum
Reign:Eukaryota
TaxID:36329
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
E26 %
F74 %


Ligand binding site composition:

B-Factor:76.099
Number of residues:35
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.0592713.500

% Hydrophobic% Polar
46.5253.48
According to VolSite

Ligand :
3jqp_6 Structure
HET Code: A2P
Formula: C10H11N5O10P2
Molecular weight: 423.169 g/mol
DrugBank ID: DB02098
Buried Surface Area:54.16 %
Polar Surface area: 263.53 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-65.684338.425611.0371


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
O5PNZLYS- 1193.670Ionic
(Protein Cationic)
C5'CBTHR- 1783.490Hydrophobic
O3'OGSER- 2472.73154.89H-Bond
(Ligand Donor)
C1'CBSER- 2474.080Hydrophobic
O1POHTYR- 2582.54120.66H-Bond
(Protein Donor)
DuArDuArTYR- 2583.620Aromatic Face/Face
C1'CE1TYR- 2583.550Hydrophobic
C1'CD1LEU- 2863.980Hydrophobic
C5'CD1LEU- 2864.260Hydrophobic
O5PNZLYS- 2873.820Ionic
(Protein Cationic)
O1POGSER- 2883.12131.12H-Bond
(Protein Donor)