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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:

2bnp

2.700 Å

X-ray

2005-03-31

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Reaction center protein L chain
ID:RCEL_RHOSH
AC:P0C0Y8
Organism:Rhodobacter sphaeroides
Reign:Bacteria
TaxID:1063
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A87 %
B9 %
C4 %


Ligand binding site composition:

B-Factor:26.097
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.544378.000

% Hydrophobic% Polar
76.7923.21
According to VolSite

Ligand :
2bnp_1 Structure
HET Code: MST
Formula: C10H19N5S
Molecular weight: 241.356 g/mol
DrugBank ID: DB08215
Buried Surface Area:65.9 %
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
99.142627.114778.9697


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
C8CBLEU- 1893.790Hydrophobic
S7CBHIS- 1903.990Hydrophobic
C15CD2LEU- 1934.210Hydrophobic
C16CBGLU- 2124.010Hydrophobic
S7CE1PHE- 2163.970Hydrophobic
C8CZPHE- 2164.20Hydrophobic
C13CE2PHE- 2163.450Hydrophobic
DuArDuArPHE- 2163.80Aromatic Face/Face
C13CG1VAL- 2204.460Hydrophobic
C11CD2TYR- 2223.680Hydrophobic
N14OGSER- 2232.99129.8H-Bond
(Ligand Donor)
C12CG2ILE- 2244.290Hydrophobic
N5NILE- 2243.17154.73H-Bond
(Protein Donor)
C16CG2THR- 2263.940Hydrophobic
C12CD1ILE- 2294.260Hydrophobic
S7CD1ILE- 2293.440Hydrophobic
C12CD2LEU- 2324.180Hydrophobic