Receptor
PDB id Resolution Class Description Source Keywords
5A8K 1.41 Å EC: 2.8.4.1 METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER WOLFEII RESOLUTION METHANOTHERMOBACTER WOLFEII 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
CA D:556;
A:562;
D:559;
A:563;
D:560;
A:565;
B:444;
D:557;
F:250;
A:564;
D:558;
E:444;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
ETX E:1452;
A:1554;
B:1446;
C:1250;
B:1445;
F:1252;
D:1552;
F:1250;
A:1552;
E:1445;
E:1448;
A:1553;
E:1446;
A:1551;
D:1551;
E:1444;
E:1450;
E:1447;
E:1449;
F:1251;
D:1553;
B:1447;
E:1451;
B:1448;
A:1555;
B:1444;
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;
submit data
90.121 C4 H10 O2 CCOCC...
COM A:556;
D:555;
Valid;
Valid;
none;
none;
submit data
142.197 C2 H6 O3 S2 C(CS(...
TP7 A:558;
D:554;
Valid;
Valid;
none;
none;
submit data
343.334 C11 H22 N O7 P S C[C@H...
K C:250;
A:566;
E:445;
D:561;
A:561;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
39.098 K [K+]
MG F:251;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
F43 D:1550;
A:1550;
Part of Protein;
Part of Protein;
none;
none;
submit data
906.58 C42 H51 N6 Ni O13 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3POT 1.2 Å EC: 2.8.4.1 STRUCTURAL ANALYSIS OF A NI(III)-METHYL SPECIES IN METHYL-CO REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS METHANOTHERMOBACTER MARBURGENSIS METAL-BINDING NICKEL METHYL-COENZYME M REDUCTASE METHANOGMETHYLATION TRANSFERASE
Ref.: STRUCTURAL ANALYSIS OF A NI-METHYL SPECIES IN METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTE MARBURGENSIS. J.AM.CHEM.SOC. V. 133 5626 2011
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 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)(=....
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 : 3POT; Ligand: COM; Similar sites found: 7
This union binding pocket(no: 1) in the query (biounit: 3pot.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2INV FRU FRU 0.04359 0.40731 6.0241
2 2OCI TYC 0.01208 0.43972 7.22892
3 1KUJ MMA 0.0218 0.43347 9.02256
4 4K7O EKZ 0.03981 0.40977 10.7143
5 3JYY PPV 0.02114 0.42313 12.0482
6 5H6S HDH 0.04394 0.407 14.8594
7 2OVD DAO 0.04421 0.40889 16.4835
Pocket No.: 2; Query (leader) PDB : 3POT; 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: 3pot.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3POT; Ligand: TP7; Similar sites found: 8
This union binding pocket(no: 3) in the query (biounit: 3pot.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2INV FRU FRU 0.04937 0.40421 6.0241
2 2OCI TYC 0.01281 0.43836 7.22892
3 1KUJ MMA 0.0199 0.43753 9.02256
4 4QS9 BGC 0.02742 0.41415 9.63855
5 3GXO MQA 0.03388 0.40925 10.0402
6 4K7O EKZ 0.03985 0.40987 10.7143
7 3JYY PPV 0.01997 0.42406 12.0482
8 2OVD DAO 0.04452 0.40873 16.4835
Pocket No.: 4; Query (leader) PDB : 3POT; Ligand: TXZ; Similar sites found: 7
This union binding pocket(no: 4) in the query (biounit: 3pot.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2INV FRU FRU 0.04359 0.40731 6.0241
2 2OCI TYC 0.01208 0.43972 7.22892
3 1KUJ MMA 0.0218 0.43347 9.02256
4 4K7O EKZ 0.03981 0.40977 10.7143
5 3JYY PPV 0.02114 0.42313 12.0482
6 5H6S HDH 0.04394 0.407 14.8594
7 2OVD DAO 0.04421 0.40889 16.4835
Pocket No.: 5; Query (leader) PDB : 3POT; Ligand: TXZ; 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: 3pot.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3POT; Ligand: TP7; 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: 3pot.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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