Receptor
PDB id Resolution Class Description Source Keywords
5A8R 2.15 Å EC: 2.8.4.1 METHYL-COENZYME M REDUCTASE II FROM METHANOTHERMOBACTER MARB AT 2.15 A RESOLUTION METHANOTHERMOBACTER MARBURGENSIS TRANSFERASE POST-TRANSLATIONAL MODIFICATION BINDING SITESCATALYSIS COENZYMES DISULFIDES HYDROGEN HYDROGEN BONDINLIGANDS MESNA METALLOPORPHYRINS METHANE METHANOBACTERIUMODELS MOLECULAR NICKEL OXIDATION-REDUCTION OXIDOREDUCTPHOSPHOTHREONINE PROTEIN CONFORMATION PROTEIN FOLDING PRSTRUCTURE
Ref.: DIDEHYDROASPARTATE MODIFICATION IN METHYL-COENZYME REDUCTASE CATALYZING METHANE FORMATION. ANGEW.CHEM.INT.ED.ENGL. V. 55 10630 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K G:604;
D:604;
D:605;
A:604;
J:604;
J:606;
J:605;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
submit data
39.098 K [K+]
COM D:601;
A:601;
G:601;
J:601;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
142.197 C2 H6 O3 S2 C(CS(...
F43 D:603;
A:603;
G:603;
J:603;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
906.58 C42 H51 N6 Ni O13 C[C@@...
TP7 G:602;
D:602;
J:602;
A:602;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
343.334 C11 H22 N O7 P S C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5A8R 2.15 Å EC: 2.8.4.1 METHYL-COENZYME M REDUCTASE II FROM METHANOTHERMOBACTER MARB AT 2.15 A RESOLUTION METHANOTHERMOBACTER MARBURGENSIS TRANSFERASE POST-TRANSLATIONAL MODIFICATION BINDING SITESCATALYSIS COENZYMES DISULFIDES HYDROGEN HYDROGEN BONDINLIGANDS MESNA METALLOPORPHYRINS METHANE METHANOBACTERIUMODELS MOLECULAR NICKEL OXIDATION-REDUCTION OXIDOREDUCTPHOSPHOTHREONINE PROTEIN CONFORMATION PROTEIN FOLDING PRSTRUCTURE
Ref.: DIDEHYDROASPARTATE MODIFICATION IN METHYL-COENZYME REDUCTASE CATALYZING METHANE FORMATION. ANGEW.CHEM.INT.ED.ENGL. V. 55 10630 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5A8R - COM C2 H6 O3 S2 C(CS(=O)(=....
2 5A8W - COM C2 H6 O3 S2 C(CS(=O)(=....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3M1V - COM C2 H6 O3 S2 C(CS(=O)(=....
2 5G0R - TP7 C11 H22 N O7 P S C[C@H]([C@....
3 3M32 - COM C2 H6 O3 S2 C(CS(=O)(=....
4 3M30 - COM C2 H6 O3 S2 C(CS(=O)(=....
5 5A0Y - TP7 C11 H22 N O7 P S C[C@H]([C@....
6 3M2R - TP7 C11 H22 N O7 P S C[C@H]([C@....
7 5A8K - COM C2 H6 O3 S2 C(CS(=O)(=....
8 3POT - COM C2 H6 O3 S2 C(CS(=O)(=....
9 3M2V - COM C2 H6 O3 S2 C(CS(=O)(=....
10 3M2U - COM C2 H6 O3 S2 C(CS(=O)(=....
11 5A8R - COM C2 H6 O3 S2 C(CS(=O)(=....
12 5A8W - COM C2 H6 O3 S2 C(CS(=O)(=....
13 5N1Q - TP7 C11 H22 N O7 P S C[C@H]([C@....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3M1V - COM C2 H6 O3 S2 C(CS(=O)(=....
2 5G0R - TP7 C11 H22 N O7 P S C[C@H]([C@....
3 3M32 - COM C2 H6 O3 S2 C(CS(=O)(=....
4 3M30 - COM C2 H6 O3 S2 C(CS(=O)(=....
5 5A0Y - TP7 C11 H22 N O7 P S C[C@H]([C@....
6 3M2R - TP7 C11 H22 N O7 P S C[C@H]([C@....
7 5A8K - COM C2 H6 O3 S2 C(CS(=O)(=....
8 3POT - COM C2 H6 O3 S2 C(CS(=O)(=....
9 3M2V - COM C2 H6 O3 S2 C(CS(=O)(=....
10 3M2U - COM C2 H6 O3 S2 C(CS(=O)(=....
11 5A8R - COM C2 H6 O3 S2 C(CS(=O)(=....
12 5A8W - COM C2 H6 O3 S2 C(CS(=O)(=....
13 3SQG - COM C2 H6 O3 S2 C(CS(=O)(=....
14 5N1Q - TP7 C11 H22 N O7 P S C[C@H]([C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: COM; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 COM 1 1
2 9SB 0.473684 0.857143
3 TAU 0.473684 0.804878
4 X1S 0.454545 0.810811
5 A20 0.409091 0.780488
Ligand no: 2; Ligand: TP7; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 TP7 1 1
2 XP8 0.979167 1
3 XP9 0.979167 1
4 TXZ 0.9375 0.979167
5 TPZ 0.857143 0.958333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5A8R; Ligand: COM; Similar sites found: 1
This union binding pocket(no: 1) in the query (biounit: 5a8r.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3BPX SAL 0.0237 0.41644 11.4865
Pocket No.: 2; Query (leader) PDB : 5A8R; Ligand: COM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5a8r.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5A8R; Ligand: TP7; Similar sites found: 6
This union binding pocket(no: 3) in the query (biounit: 5a8r.bio2) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3JYY PPV 0.02677 0.41283 4.52962
2 2INV FRU FRU 0.03421 0.41121 6.58537
3 3O8M BGC 0.03947 0.40005 6.99774
4 3O8M GLC 0.03947 0.40005 6.99774
5 2VGD XYP XYP 0.03369 0.40584 8.25688
6 5H6S HDH 0.03983 0.40731 14.717
Pocket No.: 4; Query (leader) PDB : 5A8R; Ligand: TP7; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5a8r.bio2) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5A8R; Ligand: TP7; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5a8r.bio1) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5A8R; Ligand: COM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5a8r.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5A8R; Ligand: TP7; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5a8r.bio1) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5A8R; Ligand: COM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5a8r.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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