Receptor
PDB id Resolution Class Description Source Keywords
6U4P 2.49 Å NON-ENZYME: OTHER STRUCTURE-BASED DISCOVERY OF A NOVEL SMALL-MOLECULE INHIBITO METHICILLIN-RESISTANT S. AUREUS STAPHYLOCOCCUS AUREUS ALPHA-TOXIN PVL LEUKOCIDINS MRSA TOXIN
Ref.: STRUCTURE-BASED DISCOVERY OF A SMALL-MOLECULE INHIB METHICILLIN-RESISTANTSTAPHYLOCOCCUS AUREUSVIRULENCE J.BIOL.CHEM. V. 295 5944 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PQJ D:402;
B:401;
D:401;
F:401;
C:402;
A:402;
F:402;
C:401;
B:402;
G:401;
E:402;
E:401;
A:401;
G:402;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.56;
Atoms found LESS than expected: % Diff = 0.52;
 submit data
380.523 C19 H43 N O4 P CCCCC...
SO4 G:404;
C:406;
B:404;
A:407;
B:405;
A:408;
E:406;
E:403;
A:405;
G:403;
C:405;
D:405;
F:404;
E:405;
D:404;
F:403;
D:403;
G:405;
F:406;
C:403;
A:403;
A:409;
E:407;
C:404;
F:405;
G:408;
A:406;
G:406;
B:403;
A:404;
E:404;
C:407;
G:407;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3M3R 2.2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE M113F ALPHA-HEMOLYSIN MUTANT COMPLE BETA-CYCLODEXTRIN STAPHYLOCOCCUS AUREUS BETA BARREL CYTOLYTIC PROTEIN CYTOLYSIS HEMOLYSIS SECRETTOXIN CELL INVASION
Ref.: MOLECULAR BASES OF CYCLODEXTRIN ADAPTER INTERACTION ENGINEERED PROTEIN NANOPORES. PROC.NATL.ACAD.SCI.USA V. 107 8165 2010
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 3M3R Kd = 0.000000064 M GLC GLC GLC GLC GLC GLC GLC n/a n/a
2 6U49 - PQJ C19 H43 N O4 P CCCCCCCCCC....
3 3M4E - GLC GLC GLC GLC GLC GLC GLC n/a n/a
4 6U4P - PQJ C19 H43 N O4 P CCCCCCCCCC....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 3M3R Kd = 0.000000064 M GLC GLC GLC GLC GLC GLC GLC n/a n/a
2 6U49 - PQJ C19 H43 N O4 P CCCCCCCCCC....
3 3M4E - GLC GLC GLC GLC GLC GLC GLC n/a n/a
4 6U4P - PQJ C19 H43 N O4 P CCCCCCCCCC....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 3M3R Kd = 0.000000064 M GLC GLC GLC GLC GLC GLC GLC n/a n/a
2 6U49 - PQJ C19 H43 N O4 P CCCCCCCCCC....
3 3M4E - GLC GLC GLC GLC GLC GLC GLC n/a n/a
4 6U4P - PQJ C19 H43 N O4 P CCCCCCCCCC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PQJ; Similar ligands found: 25
No: Ligand ECFP6 Tc MDL keys Tc
1 PQJ 1 1
2 LPE 0.607143 0.903846
3 DPV 0.583333 0.914894
4 K6G 0.507937 0.854545
5 LPC 0.507937 0.854545
6 LAP 0.507937 0.854545
7 LP3 0.507937 0.854545
8 SPU 0.492308 0.824561
9 PX4 0.477612 0.886792
10 HGX 0.477612 0.886792
11 PC7 0.477612 0.886792
12 6PL 0.477612 0.886792
13 PLD 0.477612 0.886792
14 HGP 0.477612 0.886792
15 LIO 0.477612 0.886792
16 CH5 0.46 0.777778
17 XP5 0.447761 0.886792
18 42H 0.444444 0.839286
19 0O8 0.423729 0.821429
20 PCW 0.421053 0.87037
21 PC 0.418605 0.836735
22 HXG 0.41791 0.886792
23 PCK 0.410256 0.839286
24 3XU 0.405063 0.770492
25 OPC 0.405063 0.854545
Similar Ligands (3D)
Ligand no: 1; Ligand: PQJ; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3M3R; Ligand: GLC GLC GLC GLC GLC GLC GLC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3m3r.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3M3R; Ligand: GLC GLC GLC GLC GLC GLC GLC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3m3r.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
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