Receptor
PDB id Resolution Class Description Source Keywords
5A0Y 1.1 Å EC: 2.8.4.1 METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURG 1.1 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
MG A:551;
D:560;
D:557;
E:445;
B:444;
C:251;
A:563;
D:551;
A:562;
B:445;
E:444;
E:446;
F:251;
C:250;
F:250;
A:553;
 Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
Invalid;
Part of Protein;
Invalid;
Invalid;
Part of Protein;
Invalid;
Invalid;
Invalid;
Part of Protein;
Part of Protein;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
24.305 Mg [Mg+2...
F43 D:552;
A:554;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
906.58 C42 H51 N6 Ni O13 C[C@@...
TP7 A:557;
D:556;
 Valid;
Valid;
 none;
none;
 submit data
343.334 C11 H22 N O7 P S C[C@H...
NA D:558;
A:564;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
22.99 Na [Na+]
COM D:555;
A:555;
 Valid;
Valid;
 none;
none;
 submit data
142.197 C2 H6 O3 S2 C(CS(...
CL A:565;
D:559;
 Invalid;
Invalid;
 none;
none;
 submit data
35.453 Cl [Cl-]
K A:561;
 Part of Protein;
 none;
 submit data
39.098 K [K+]
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 (2D)
Ligand no: 1; Ligand: TP7; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 TP7 1 1
2 XP9 0.979167 1
3 XP8 0.979167 1
4 TXZ 0.9375 0.979167
5 TPZ 0.857143 0.958333
Ligand no: 2; Ligand: COM; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 COM 1 1
2 8X3 0.5 0.891892
3 TAU 0.473684 0.804878
4 9SB 0.473684 0.857143
5 X1S 0.454545 0.810811
6 A20 0.409091 0.780488
Similar Ligands (3D)
Ligand no: 1; Ligand: TP7; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: COM; Similar ligands found: 231
No: Ligand Similarity coefficient
1 ETM 1.0000
2 P7I 1.0000
3 2HE 1.0000
4 POA 1.0000
5 EFS 1.0000
6 VX 1.0000
7 CHT 1.0000
8 XPO 0.9971
9 FJO 0.9966
10 BTL 0.9813
11 OPE 0.9759
12 7VD 0.9675
13 PGA 0.9652
14 ODV 0.9611
15 S0H 0.9608
16 PCT 0.9590
17 PAE 0.9566
18 FCN 0.9565
19 TB6 0.9561
20 1SP 0.9553
21 MPD 0.9544
22 HSW 0.9538
23 SAT 0.9537
24 CP 0.9536
25 FW5 0.9514
26 TB0 0.9507
27 DSS 0.9505
28 ETF 0.9466
29 BMD 0.9457
30 BAE 0.9448
31 BU4 0.9445
32 SGL 0.9430
33 TAY 0.9407
34 MMQ 0.9396
35 HLT 0.9370
36 BAL 0.9365
37 VSO 0.9365
38 CNH 0.9348
39 BUA 0.9345
40 MTG 0.9335
41 PPF 0.9323
42 BUB 0.9322
43 DTL 0.9310
44 3OH 0.9305
45 TAN 0.9300
46 SLP 0.9290
47 ITU 0.9289
48 MLA 0.9289
49 HV2 0.9286
50 MLI 0.9277
51 SAR 0.9273
52 BUQ 0.9266
53 SSN 0.9240
54 EGD 0.9228
55 NVA 0.9202
56 LER 0.9193
57 MSF 0.9185
58 DTT 0.9178
59 AOA 0.9173
60 LLQ 0.9167
61 1GP 0.9164
62 8FH 0.9164
63 HSE 0.9159
64 ETX 0.9147
65 SMB 0.9146
66 PAH 0.9142
67 1SH 0.9138
68 PRI 0.9133
69 HCS 0.9131
70 LEA 0.9129
71 ABU 0.9128
72 G3P 0.9124
73 BXO 0.9123
74 9X7 0.9122
75 PUT 0.9114
76 3BB 0.9114
77 DAB 0.9114
78 IHG 0.9108
79 THR 0.9103
80 DE2 0.9102
81 MTD 0.9102
82 1AC 0.9097
83 CYS 0.9092
84 GG6 0.9091
85 SIN 0.9079
86 39J 0.9074
87 9YL 0.9073
88 XAP 0.9061
89 3PY 0.9056
90 MRY 0.9049
91 ICN 0.9045
92 SER 0.9043
93 HUI 0.9039
94 A8C 0.9036
95 HX2 0.9033
96 DTU 0.9029
97 3HR 0.9028
98 MAE 0.9021
99 DMG 0.9017
100 DXX 0.9017
101 PRO 0.9016
102 C2N 0.9016
103 IPU 0.9012
104 A3B 0.9010
105 4HA 0.9010
106 PE9 0.9009
107 IVA 0.9008
108 DCY 0.9004
109 3GR 0.9003
110 3HL 0.9002
111 2RA 0.8996
112 HIU 0.8989
113 ASN 0.8989
114 KG7 0.8989
115 192 0.8984
116 VAL 0.8982
117 03W 0.8979
118 ILE 0.8972
119 3SS 0.8966
120 AML 0.8956
121 2KT 0.8955
122 CSS 0.8954
123 DSN 0.8951
124 ASP 0.8948
125 ORN 0.8944
126 4MV 0.8935
127 1KA 0.8930
128 DBB 0.8927
129 NVI 0.8924
130 DGY 0.8916
131 GXV 0.8915
132 GOL 0.8915
133 POP 0.8910
134 AAE 0.8908
135 PPV 0.8907
136 TFB 0.8905
137 MLM 0.8904
138 FLA 0.8898
139 NCM 0.8889
140 3PP 0.8885
141 P2D 0.8880
142 HE2 0.8878
143 DCL 0.8878
144 PPI 0.8877
145 ABA 0.8877
146 LEU 0.8875
147 GLY 0.8875
148 2PN 0.8874
149 1DU 0.8865
150 C5J 0.8863
151 2RH 0.8859
152 ISU 0.8856
153 R3W 0.8853
154 PIS 0.8849
155 6NA 0.8849
156 HSM 0.8847
157 HVQ 0.8845
158 JYD 0.8845
159 MZ0 0.8841
160 AHR 0.8841
161 MET 0.8839
162 F3V 0.8835
163 MDN 0.8834
164 2EZ 0.8833
165 FAH 0.8833
166 1BP 0.8826
167 BVC 0.8825
168 THE 0.8822
169 HDA 0.8819
170 DZZ 0.8812
171 NIE 0.8811
172 CIZ 0.8804
173 BXA 0.8796
174 BVG 0.8796
175 DPF 0.8792
176 DAS 0.8790
177 MLT 0.8789
178 TEO 0.8789
179 AKR 0.8783
180 GOA 0.8777
181 E60 0.8772
182 MSE 0.8771
183 GLV 0.8758
184 23W 0.8757
185 ALO 0.8750
186 NMG 0.8748
187 R1X 0.8748
188 2CO 0.8738
189 MED 0.8738
190 2MH 0.8738
191 4JU 0.8738
192 PXO 0.8737
193 MEU 0.8735
194 COI 0.8731
195 AKB 0.8729
196 FUM 0.8726
197 PYZ 0.8726
198 LMR 0.8716
199 BYZ 0.8703
200 1DQ 0.8690
201 AMC 0.8684
202 3CL 0.8684
203 CRD 0.8679
204 ES3 0.8679
205 PG3 0.8674
206 PAF 0.8657
207 NMU 0.8652
208 LDU 0.8651
209 TZZ 0.8648
210 OHG 0.8644
211 HVB 0.8642
212 SYN 0.8639
213 HZP 0.8638
214 2PC 0.8633
215 9A7 0.8632
216 J3K 0.8630
217 MZW 0.8617
218 CEJ 0.8612
219 ABN 0.8611
220 1CB 0.8611
221 CMS 0.8610
222 ATQ 0.8609
223 PYJ 0.8594
224 FSG 0.8589
225 OAA 0.8584
226 13D 0.8576
227 1MR 0.8573
228 BP9 0.8561
229 CP2 0.8553
230 PEP 0.8539
231 ICF 0.8528
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3POT; Ligand: COM; 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: 3pot.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3POT; Ligand: COM; 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: 3pot.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3POT; Ligand: TP7; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3pot.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3POT; Ligand: TXZ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3pot.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3POT; Ligand: TXZ; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3POT; Ligand: TP7; Similar sites found with APoc: 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 Sequence Similarity
APoc FAQ
Feedback