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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:

1dxr

2.000 Å

X-ray

2000-01-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Reaction center protein L chain
ID:RCEL_BLAVI
AC:P06009
Organism:Blastochloris viridis
Reign:Bacteria
TaxID:1079
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
H4 %
L92 %
M4 %


Ligand binding site composition:

B-Factor:23.303
Number of residues:28
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.406330.750

% Hydrophobic% Polar
72.4527.55
According to VolSite

Ligand :
1dxr_1 Structure
HET Code: MST
Formula: C10H19N5S
Molecular weight: 241.356 g/mol
DrugBank ID: DB08215
Buried Surface Area:66.54 %
Polar Surface area: 88.03 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 2
Rings: 1
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
131.42569.3562-3.47269


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
C8CBALA- 1864.430Hydrophobic
C8CBLEU- 1893.360Hydrophobic
S7CBHIS- 1903.970Hydrophobic
C15CD2LEU- 1933.80Hydrophobic
C16CBGLU- 2123.870Hydrophobic
S7CE2PHE- 2164.050Hydrophobic
C13CD1PHE- 2163.830Hydrophobic
DuArDuArPHE- 2163.850Aromatic Face/Face
C11CG2VAL- 2204.020Hydrophobic
C13CG2VAL- 2204.090Hydrophobic
N9OTYR- 2223.31157.95H-Bond
(Ligand Donor)
C11CD2TYR- 2223.920Hydrophobic
N14OGSER- 2232.95166.32H-Bond
(Ligand Donor)
N5NILE- 2243.08162.61H-Bond
(Protein Donor)
S7CD1ILE- 2293.650Hydrophobic
C12CD2LEU- 2324.460Hydrophobic