Receptor
PDB id Resolution Class Description Source Keywords
5REQ 2.2 Å EC: 5.4.99.2 METHYLMALONYL-COA MUTASE, Y89F MUTANT, SUBSTRATE COMPLEX PROPIONIBACTERIUM FREUDENREICHII SUBSPSHERMANII ISOMERASE MUTASE INTRAMOLECULAR TRANSFERASE
Ref.: STABILIZATION OF RADICAL INTERMEDIATES BY AN ACTIVE TYROSINE RESIDUE IN METHYLMALONYL-COA MUTASE. BIOCHEMISTRY V. 37 14386 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
B12 A:1800;
C:2800;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
1330.36 C62 H89 Co N13 O14 P Cc1cc...
GOL B:3001;
B:3002;
D:3003;
D:3004;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
MCD A:1802;
C:2802;
 Valid;
Valid;
 none;
none;
 submit data
849.568 C26 H42 N7 O19 P3 C[C@@...
SCD A:1801;
C:2801;
 Valid;
Valid;
 none;
none;
 submit data
849.568 C26 H42 N7 O19 P3 CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1REQ 2 Å EC: 5.4.99.2 METHYLMALONYL-COA MUTASE PROPIONIBACTERIUM FREUDENREICHII SUBSPSHERMANII ISOMERASE MUTASE INTRAMOLECULAR TRANSFERASE
Ref.: HOW COENZYME B12 RADICALS ARE GENERATED: THE CRYSTA STRUCTURE OF METHYLMALONYL-COENZYME A MUTASE AT 2 A RESOLUTION. STRUCTURE V. 4 339 1996
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6REQ - 3CP C25 H42 N7 O18 P3 S CC(C)(CO[P....
2 2REQ - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 5REQ - MCD C26 H42 N7 O19 P3 C[C@@H](C(....
4 4REQ - MCA C25 H40 N7 O19 P3 S C[C@H](C(=....
5 7REQ - 2CP C25 H42 N7 O18 P3 S C[C@@H](CS....
6 1REQ - DCA C21 H36 N7 O16 P3 CCNC(=O)CC....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6REQ - 3CP C25 H42 N7 O18 P3 S CC(C)(CO[P....
2 2REQ - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 5REQ - MCD C26 H42 N7 O19 P3 C[C@@H](C(....
4 4REQ - MCA C25 H40 N7 O19 P3 S C[C@H](C(=....
5 7REQ - 2CP C25 H42 N7 O18 P3 S C[C@@H](CS....
6 1REQ - DCA C21 H36 N7 O16 P3 CCNC(=O)CC....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6REQ - 3CP C25 H42 N7 O18 P3 S CC(C)(CO[P....
2 2REQ - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 5REQ - MCD C26 H42 N7 O19 P3 C[C@@H](C(....
4 4REQ - MCA C25 H40 N7 O19 P3 S C[C@H](C(=....
5 7REQ - 2CP C25 H42 N7 O18 P3 S C[C@@H](CS....
6 1REQ - DCA C21 H36 N7 O16 P3 CCNC(=O)CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MCD; Similar ligands found: 183
No: Ligand ECFP6 Tc MDL keys Tc
1 MCD 1 1
2 CMX 0.884298 0.977012
3 AMX 0.876033 0.965517
4 HAX 0.854839 0.933333
5 SCD 0.84252 0.977012
6 COA 0.836066 0.954545
7 0T1 0.836066 0.954545
8 DCA 0.834711 0.954545
9 FCX 0.832 0.944444
10 30N 0.830645 0.875
11 CA6 0.826772 0.886598
12 SCO 0.824 0.977012
13 NMX 0.820312 0.884211
14 ETB 0.819672 0.943182
15 FAM 0.81746 0.933333
16 COS 0.816 0.933333
17 CAO 0.816 0.923077
18 MCA 0.815385 0.966292
19 CAJ 0.813953 0.977273
20 2CP 0.80916 0.966292
21 CMC 0.806202 0.955056
22 ACO 0.80315 0.966292
23 YZS 0.79845 0.867347
24 OXK 0.79845 0.955056
25 KGP 0.79845 0.867347
26 SOP 0.79845 0.955056
27 A1S 0.793893 0.955056
28 CO6 0.792308 0.955056
29 3KK 0.790698 0.955056
30 FYN 0.790698 0.954545
31 CA8 0.789474 0.848485
32 3CP 0.789474 0.955056
33 COK 0.784615 0.933333
34 SCA 0.781955 0.955056
35 MLC 0.780303 0.955056
36 3HC 0.780303 0.94382
37 IVC 0.780303 0.94382
38 1VU 0.778626 0.944444
39 COF 0.776119 0.913043
40 SO5 0.774436 0.877551
41 LCV 0.774436 0.877551
42 2MC 0.772727 0.913979
43 YXS 0.768657 0.867347
44 YXR 0.768657 0.867347
45 KGJ 0.766917 0.894737
46 BCO 0.766917 0.933333
47 1HE 0.766917 0.934066
48 GRA 0.764706 0.955056
49 2KQ 0.762963 0.977528
50 HGG 0.762963 0.955056
51 IRC 0.762963 0.94382
52 YE1 0.761194 0.94382
53 CAA 0.761194 0.94382
54 COO 0.761194 0.933333
55 TGC 0.759124 0.944444
56 4CA 0.757353 0.923077
57 MC4 0.755556 0.904255
58 CIC 0.753623 0.955056
59 HXC 0.751825 0.955556
60 KGA 0.75 0.905263
61 BYC 0.75 0.933333
62 COW 0.75 0.923077
63 KFV 0.75 0.876289
64 1GZ 0.75 0.923077
65 BCA 0.744526 0.923077
66 FAQ 0.744526 0.933333
67 0ET 0.742857 0.955556
68 CO8 0.741007 0.955556
69 S0N 0.741007 0.955056
70 1CZ 0.741007 0.944444
71 2NE 0.741007 0.913043
72 CS8 0.737589 0.945055
73 5F9 0.735714 0.955556
74 DCC 0.735714 0.955556
75 MFK 0.735714 0.955556
76 0FQ 0.735714 0.933333
77 UCC 0.735714 0.955556
78 MYA 0.735714 0.955556
79 4CO 0.735714 0.923077
80 ST9 0.735714 0.955556
81 UOQ 0.732394 0.955556
82 NHW 0.732394 0.955556
83 NHM 0.732394 0.955556
84 01A 0.730496 0.893617
85 MRS 0.727273 0.955556
86 MRR 0.727273 0.955556
87 1CV 0.725352 0.955056
88 HDC 0.72028 0.955556
89 NHQ 0.719178 0.94382
90 HFQ 0.715278 0.913043
91 WCA 0.713287 0.913043
92 YNC 0.710345 0.923077
93 4KX 0.708333 0.903226
94 8Z2 0.705479 0.945055
95 01K 0.704698 0.955056
96 J5H 0.69863 0.933333
97 DAK 0.69863 0.903226
98 CA3 0.679739 0.933333
99 COT 0.677632 0.933333
100 COD 0.676923 0.943182
101 1HA 0.675497 0.913043
102 93P 0.675159 0.944444
103 F8G 0.666667 0.935484
104 93M 0.664596 0.944444
105 CCQ 0.657534 0.913979
106 7L1 0.652174 0.966292
107 CA5 0.647799 0.893617
108 N9V 0.635135 0.902174
109 UCA 0.63354 0.955556
110 CO7 0.627586 0.933333
111 COA FLC 0.618705 0.921348
112 OXT 0.604651 0.914894
113 4BN 0.588571 0.914894
114 5TW 0.588571 0.914894
115 JBT 0.581006 0.915789
116 BSJ 0.574713 0.923913
117 PAP 0.563025 0.793103
118 PLM COA 0.55414 0.923077
119 COA PLM 0.55414 0.923077
120 HMG 0.551282 0.922222
121 ASP ASP ASP ILE CMC NH2 0.538462 0.912088
122 A3P 0.512605 0.781609
123 PPS 0.512 0.71875
124 ACE SER ASP ALY THR NH2 COA 0.502732 0.933333
125 0WD 0.493151 0.771739
126 SFC 0.48503 0.934066
127 RFC 0.48503 0.934066
128 191 0.465839 0.848485
129 PTJ 0.463235 0.873563
130 3AM 0.45 0.770115
131 48N 0.441379 0.831461
132 A22 0.440298 0.795455
133 PUA 0.43871 0.802198
134 F2R 0.437086 0.866667
135 A2D 0.435484 0.784091
136 PAJ 0.433824 0.885057
137 HQG 0.432836 0.816092
138 YLB 0.432432 0.909091
139 3OD 0.431655 0.827586
140 AGS 0.430769 0.769231
141 SAP 0.430769 0.769231
142 ATR 0.430769 0.781609
143 9BG 0.427632 0.771739
144 ADP 0.425197 0.804598
145 A2R 0.422222 0.816092
146 YLP 0.421769 0.909091
147 TXA 0.421429 0.818182
148 8LE 0.421053 0.850575
149 8LQ 0.419118 0.83908
150 BA3 0.417323 0.784091
151 NA7 0.417266 0.83908
152 OAD 0.417266 0.827586
153 HEJ 0.415385 0.804598
154 ATP 0.415385 0.804598
155 B4P 0.414062 0.784091
156 AP5 0.414062 0.784091
157 AR6 0.412214 0.804598
158 APR 0.412214 0.804598
159 2A5 0.412214 0.827586
160 AQP 0.412214 0.804598
161 5FA 0.412214 0.804598
162 BIS 0.411348 0.8
163 AN2 0.410853 0.795455
164 5AL 0.410448 0.816092
165 M33 0.407692 0.795455
166 ATF 0.407407 0.777778
167 A A A 0.407143 0.795455
168 9X8 0.407143 0.788889
169 OMR 0.406667 0.897727
170 8QN 0.405797 0.816092
171 KG4 0.40458 0.806818
172 8LH 0.404412 0.83908
173 SRP 0.404412 0.83908
174 WAQ 0.404255 0.862069
175 J4G 0.404255 0.850575
176 ANP 0.402985 0.786517
177 ADQ 0.402878 0.806818
178 NB8 0.401408 0.811111
179 1ZZ 0.401408 0.886364
180 APU 0.401316 0.769231
181 NJP 0.4 0.788889
182 AHX 0.4 0.811111
183 AT4 0.4 0.777778
Ligand no: 2; Ligand: SCD; Similar ligands found: 170
No: Ligand ECFP6 Tc MDL keys Tc
1 SCD 1 1
2 CMX 0.900826 1
3 AMX 0.861789 0.988235
4 SCO 0.854839 1
5 MCD 0.84252 0.977012
6 HAX 0.84127 0.954545
7 COA 0.822581 0.976744
8 0T1 0.822581 0.976744
9 DCA 0.821138 0.954023
10 30N 0.81746 0.893617
11 CAO 0.81746 0.94382
12 COS 0.81746 0.954545
13 CA6 0.813953 0.865979
14 SCA 0.810606 0.977012
15 NMX 0.807692 0.903226
16 CMC 0.807692 0.977012
17 ETB 0.806452 0.920455
18 ACO 0.804688 0.94382
19 FCX 0.804688 0.965909
20 3CP 0.804511 0.977012
21 CAJ 0.801527 0.977012
22 OXK 0.8 0.977012
23 MLC 0.795455 0.977012
24 CO6 0.793893 0.954545
25 GRA 0.792593 0.977012
26 FYN 0.792308 0.976744
27 3KK 0.792308 0.954545
28 FAM 0.790698 0.954545
29 COK 0.78626 0.954545
30 SOP 0.78626 0.954545
31 A1S 0.781955 0.954545
32 1VU 0.780303 0.94382
33 2KQ 0.777778 0.955056
34 HGG 0.777778 0.977012
35 CA8 0.777778 0.865979
36 MCA 0.776119 0.965909
37 2MC 0.774436 0.913043
38 KGP 0.772727 0.865979
39 YZS 0.772727 0.865979
40 MC4 0.77037 0.903226
41 2CP 0.77037 0.965909
42 KGJ 0.768657 0.893617
43 1HE 0.768657 0.933333
44 BCO 0.768657 0.954545
45 IVC 0.768657 0.965517
46 3HC 0.768657 0.965517
47 1CZ 0.768116 0.965909
48 KFV 0.764706 0.875
49 COF 0.764706 0.933333
50 COO 0.762963 0.954545
51 CAA 0.762963 0.965517
52 TGC 0.76087 0.965909
53 BCA 0.759124 0.94382
54 YXR 0.757353 0.865979
55 YXS 0.757353 0.865979
56 CIC 0.755396 0.977012
57 HXC 0.753623 0.933333
58 KGA 0.751825 0.904255
59 BYC 0.751825 0.954545
60 COW 0.751825 0.94382
61 IRC 0.751825 0.965517
62 1GZ 0.751825 0.94382
63 1CV 0.751773 0.977012
64 LCV 0.75 0.876289
65 YE1 0.75 0.965517
66 SO5 0.75 0.876289
67 NHW 0.746479 0.933333
68 NHM 0.746479 0.933333
69 UOQ 0.746479 0.933333
70 4CA 0.746377 0.94382
71 FAQ 0.746377 0.954545
72 CO8 0.742857 0.933333
73 MFK 0.737589 0.933333
74 DCC 0.737589 0.933333
75 5F9 0.737589 0.933333
76 MYA 0.737589 0.933333
77 ST9 0.737589 0.933333
78 UCC 0.737589 0.933333
79 0ET 0.732394 0.933333
80 2NE 0.730496 0.933333
81 S0N 0.730496 0.977012
82 CS8 0.727273 0.923077
83 4CO 0.725352 0.94382
84 0FQ 0.725352 0.954545
85 HDC 0.722222 0.933333
86 01A 0.72028 0.913043
87 MRR 0.717241 0.933333
88 MRS 0.717241 0.933333
89 WCA 0.715278 0.933333
90 YNC 0.712329 0.94382
91 4KX 0.710345 0.923077
92 NHQ 0.709459 0.965517
93 8Z2 0.707483 0.923077
94 HFQ 0.705479 0.933333
95 J5H 0.70068 0.954545
96 DAK 0.70068 0.923077
97 01K 0.695364 0.954545
98 1HA 0.677632 0.933333
99 CA3 0.670968 0.954545
100 COT 0.668831 0.954545
101 F8G 0.668831 0.913979
102 COD 0.666667 0.965116
103 CCQ 0.659864 0.913043
104 93P 0.65625 0.965909
105 7L1 0.654676 0.94382
106 93M 0.646341 0.965909
107 UCA 0.645963 0.933333
108 CA5 0.639752 0.913043
109 CO7 0.630137 0.954545
110 N9V 0.626667 0.922222
111 COA FLC 0.609929 0.942529
112 OXT 0.597701 0.893617
113 JBT 0.583333 0.894737
114 5TW 0.581921 0.893617
115 4BN 0.581921 0.893617
116 BSJ 0.577143 0.944444
117 HMG 0.564103 0.943182
118 COA PLM 0.556962 0.901099
119 PLM COA 0.556962 0.901099
120 PAP 0.553719 0.811765
121 ASP ASP ASP ILE CMC NH2 0.532164 0.932584
122 A3P 0.504132 0.8
123 PPS 0.503937 0.734043
124 ACE SER ASP ALY THR NH2 COA 0.497297 0.932584
125 0WD 0.486486 0.788889
126 191 0.478261 0.846939
127 SFC 0.470588 0.933333
128 RFC 0.470588 0.933333
129 PTJ 0.446043 0.894118
130 3AM 0.442623 0.788235
131 A22 0.433824 0.813953
132 PUA 0.433121 0.820225
133 A2D 0.428571 0.802326
134 WAQ 0.428571 0.882353
135 PAJ 0.427536 0.905882
136 YLB 0.426667 0.930233
137 HQG 0.426471 0.835294
138 48N 0.425676 0.829545
139 3OD 0.425532 0.847059
140 AGS 0.424242 0.786517
141 ATR 0.424242 0.8
142 SAP 0.424242 0.786517
143 9BG 0.422078 0.788889
144 NJP 0.422078 0.806818
145 F2R 0.422078 0.886364
146 ADP 0.418605 0.823529
147 J4G 0.41844 0.870588
148 YLP 0.416107 0.908046
149 A2R 0.416058 0.835294
150 8LE 0.414815 0.870588
151 8LQ 0.413043 0.858824
152 NA7 0.411348 0.858824
153 OAD 0.411348 0.847059
154 BA3 0.410853 0.802326
155 HEJ 0.409091 0.823529
156 ATP 0.409091 0.823529
157 SRP 0.408759 0.858824
158 AP5 0.407692 0.802326
159 B4P 0.407692 0.802326
160 5FA 0.406015 0.823529
161 2A5 0.406015 0.847059
162 APR 0.406015 0.823529
163 AQP 0.406015 0.823529
164 AR6 0.406015 0.823529
165 1ZZ 0.405594 0.863636
166 AN2 0.40458 0.813953
167 DLL 0.404255 0.813953
168 M33 0.401515 0.813953
169 9X8 0.401408 0.806818
170 LAQ 0.4 0.822222
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1REQ; Ligand: DCA; 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: 1req.bio2) has 43 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1REQ; Ligand: DCA; 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: 1req.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
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