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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:

2bl9

1.900 Å

X-ray

2005-03-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Bifunctional dihydrofolate reductase-thymidylate synthase
ID:DRTS_PLAVI
AC:O02604
Organism:Plasmodium vivax
Reign:Eukaryota
TaxID:5855
EC Number:1.5.1.3


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:31.446
Number of residues:30
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: NDP
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.628658.125

% Hydrophobic% Polar
66.6733.33
According to VolSite

Ligand :
2bl9_1 Structure
HET Code: CP6
Formula: C12H13ClN4
Molecular weight: 248.711 g/mol
DrugBank ID: DB00205
Buried Surface Area:70.83 %
Polar Surface area: 77.81 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
89.757512.897234.0574


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
N13OILE- 132.94167.2H-Bond
(Ligand Donor)
N14OCYS- 143.16120.5H-Bond
(Ligand Donor)
C15CD1LEU- 454.050Hydrophobic
C12CD2LEU- 453.80Hydrophobic
N6OD2ASP- 532.61161.02H-Bond
(Ligand Donor)
N14OD1ASP- 532.86170.48H-Bond
(Ligand Donor)
C16SDMET- 543.840Hydrophobic
C16CBPHE- 574.070Hydrophobic
CL1CBSER- 1173.660Hydrophobic
CL1CG1ILE- 1213.550Hydrophobic
C8CBILE- 1734.280Hydrophobic
C9CD1ILE- 1734.090Hydrophobic
N13OILE- 1732.95131.17H-Bond
(Ligand Donor)