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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:

6prc

2.300 Å

X-ray

1997-07-31

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
L91 %
M4 %
H4 %


Ligand binding site composition:

B-Factor:25.470
Number of residues:27
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.224347.625

% Hydrophobic% Polar
72.8227.18
According to VolSite

Ligand :
6prc_1 Structure
HET Code: CEB
Formula: C10H15ClN6
Molecular weight: 254.719 g/mol
DrugBank ID: DB07551
Buried Surface Area:60.93 %
Polar Surface area: 86.52 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
131.46268.764-3.81365


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
CL2CBLEU- 1893.780Hydrophobic
CL2CBHIS- 1904.360Hydrophobic
C14CD2LEU- 1933.890Hydrophobic
C15CBGLU- 2124.030Hydrophobic
CL2CZPHE- 2163.920Hydrophobic
C8CD1PHE- 2164.40Hydrophobic
DuArDuArPHE- 2163.760Aromatic Face/Face
C10CG2VAL- 2203.670Hydrophobic
N7OTYR- 2223.14135.07H-Bond
(Ligand Donor)
C10CD2TYR- 2224.050Hydrophobic
N13OGSER- 2232.86163.93H-Bond
(Ligand Donor)
N5NILE- 2242.91161.43H-Bond
(Protein Donor)
C15CBALA- 2264.420Hydrophobic
CL2CD1ILE- 2293.760Hydrophobic
C12CD2LEU- 2324.470Hydrophobic