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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:

1rjg

2.610 Å

X-ray

2003-11-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Leucine carboxyl methyltransferase 1
ID:LCMT1_YEAST
AC:Q04081
Organism:Saccharomyces cerevisiae
Reign:Eukaryota
TaxID:559292
EC Number:2.1.1.233


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:47.871
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.536688.500

% Hydrophobic% Polar
43.1456.86
According to VolSite

Ligand :
1rjg_1 Structure
HET Code: SAH
Formula: C14H20N6O5S
Molecular weight: 384.411 g/mol
DrugBank ID: DB01752
Buried Surface Area:69.8 %
Polar Surface area: 212.38 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
17.312243.896631.0825


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
SDCBASP- 94.230Hydrophobic
C3'CBASP- 94.10Hydrophobic
CGCBALA- 124.040Hydrophobic
ONH2ARG- 813.1121.61H-Bond
(Protein Donor)
OCZARG- 813.950Ionic
(Protein Cationic)
NOGLY- 1052.8155.61H-Bond
(Ligand Donor)
O3'OD2ASP- 1283.33174.31H-Bond
(Ligand Donor)
O2'OD1ASP- 1282.53161.65H-Bond
(Ligand Donor)
DuArDuArTYR- 1293.790Aromatic Face/Face
O2'OGSER- 1323.42124.5H-Bond
(Protein Donor)
N6OD1ASP- 1753.43146.63H-Bond
(Ligand Donor)
N1NLEU- 1763.39175.59H-Bond
(Protein Donor)
NOGLU- 2012.64122.54H-Bond
(Ligand Donor)
NOE1GLU- 2013.790Ionic
(Ligand Cationic)
CGCBCYS- 2023.980Hydrophobic
C1'CD1LEU- 2034.180Hydrophobic
C5'CE1TYR- 2064.10Hydrophobic