Receptor
PDB id Resolution Class Description Source Keywords
3M1V 1.45 Å EC: 2.8.4.1 STRUCTURAL INSIGHT INTO METHYL-COENZYME M REDUCTASE CHEMISTR COENZYME B ANALOGUES METHANOTHERMOBACTER MARBURGENSIS METHYL-COENZYME M REDUCTASE METAL-BINDING METHANOGENESIS METHYLATION NICKEL TRANSFERASE
Ref.: STRUCTURAL INSIGHT INTO METHYL-COENZYME M REDUCTASE CHEMISTRY USING COENZYME B ANALOGUES. BIOCHEMISTRY V. 49 7683 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:555;
A:556;
B:446;
C:1;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
COM A:554;
D:554;
Valid;
Valid;
none;
none;
submit data
142.197 C2 H6 O3 S2 C(CS(...
EDO D:555;
F:251;
F:252;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
F43 A:1;
D:552;
Part of Protein;
Part of Protein;
none;
none;
submit data
906.58 C42 H51 N6 Ni O13 C[C@@...
MG A:551;
A:552;
B:444;
B:445;
C:250;
D:1;
D:551;
E:444;
F:250;
Part of Protein;
Part of Protein;
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;
none;
none;
submit data
24.305 Mg [Mg+2...
PEG A:557;
C:251;
Invalid;
Invalid;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
TP7 A:553;
D:553;
Valid;
Valid;
none;
none;
submit data
343.334 C11 H22 N O7 P S C[C@H...
ZN A:558;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
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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