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 2 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 2 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 2 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: 164
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 0T1 0.836066 0.954545
7 COA 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 CAO 0.816 0.923077
17 COS 0.816 0.933333
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 SOP 0.79845 0.955056
24 OXK 0.79845 0.955056
25 A1S 0.793893 0.955056
26 CO6 0.792308 0.955056
27 FYN 0.790698 0.954545
28 3KK 0.790698 0.955056
29 3CP 0.789474 0.955056
30 CA8 0.789474 0.848485
31 COK 0.784615 0.933333
32 SCA 0.781955 0.955056
33 MLC 0.780303 0.955056
34 3HC 0.780303 0.94382
35 IVC 0.780303 0.94382
36 1VU 0.778626 0.944444
37 COF 0.776119 0.913043
38 2MC 0.772727 0.913979
39 1HE 0.766917 0.934066
40 BCO 0.766917 0.933333
41 GRA 0.764706 0.955056
42 IRC 0.762963 0.94382
43 HGG 0.762963 0.955056
44 2KQ 0.762963 0.977528
45 CAA 0.761194 0.94382
46 YE1 0.761194 0.94382
47 COO 0.761194 0.933333
48 TGC 0.759124 0.944444
49 4CA 0.757353 0.923077
50 MC4 0.755556 0.904255
51 CIC 0.753623 0.955056
52 HXC 0.751825 0.955556
53 COW 0.75 0.923077
54 1GZ 0.75 0.923077
55 BYC 0.75 0.933333
56 BCA 0.744526 0.923077
57 FAQ 0.744526 0.933333
58 0ET 0.742857 0.955556
59 1CZ 0.741007 0.944444
60 S0N 0.741007 0.955056
61 CO8 0.741007 0.955556
62 2NE 0.741007 0.913043
63 CS8 0.737589 0.945055
64 MFK 0.735714 0.955556
65 DCC 0.735714 0.955556
66 5F9 0.735714 0.955556
67 UCC 0.735714 0.955556
68 MYA 0.735714 0.955556
69 0FQ 0.735714 0.933333
70 ST9 0.735714 0.955556
71 4CO 0.735714 0.923077
72 NHM 0.732394 0.955556
73 NHW 0.732394 0.955556
74 UOQ 0.732394 0.955556
75 01A 0.730496 0.893617
76 MRS 0.727273 0.955556
77 MRR 0.727273 0.955556
78 1CV 0.725352 0.955056
79 HDC 0.72028 0.955556
80 NHQ 0.719178 0.94382
81 HFQ 0.715278 0.913043
82 WCA 0.713287 0.913043
83 YNC 0.710345 0.923077
84 4KX 0.708333 0.903226
85 8Z2 0.705479 0.945055
86 01K 0.704698 0.955056
87 DAK 0.69863 0.903226
88 CA3 0.679739 0.933333
89 COT 0.677632 0.933333
90 COD 0.676923 0.943182
91 1HA 0.675497 0.913043
92 93P 0.675159 0.944444
93 F8G 0.666667 0.935484
94 93M 0.664596 0.944444
95 CCQ 0.657534 0.913979
96 7L1 0.652174 0.966292
97 CA5 0.647799 0.893617
98 UCA 0.63354 0.955556
99 CO7 0.627586 0.933333
100 OXT 0.604651 0.914894
101 5TW 0.588571 0.914894
102 4BN 0.588571 0.914894
103 JBT 0.581006 0.915789
104 BSJ 0.574713 0.923913
105 PAP 0.563025 0.793103
106 PLM COA 0.55414 0.923077
107 COA PLM 0.55414 0.923077
108 HMG 0.551282 0.922222
109 ASP ASP ASP ILE CMC NH2 0.538462 0.912088
110 A3P 0.512605 0.781609
111 PPS 0.512 0.71875
112 ACE SER ASP ALY THR NH2 COA 0.502732 0.933333
113 0WD 0.493151 0.771739
114 SFC 0.48503 0.934066
115 RFC 0.48503 0.934066
116 191 0.465839 0.848485
117 PTJ 0.463235 0.873563
118 3AM 0.45 0.770115
119 48N 0.441379 0.831461
120 A22 0.440298 0.795455
121 PUA 0.43871 0.802198
122 F2R 0.437086 0.866667
123 A2D 0.435484 0.784091
124 PAJ 0.433824 0.885057
125 YLB 0.432432 0.909091
126 3OD 0.431655 0.827586
127 AGS 0.430769 0.769231
128 SAP 0.430769 0.769231
129 ATR 0.430769 0.781609
130 ADP 0.425197 0.804598
131 A2R 0.422222 0.816092
132 YLP 0.421769 0.909091
133 TXA 0.421429 0.818182
134 BA3 0.417323 0.784091
135 NA7 0.417266 0.83908
136 OAD 0.417266 0.827586
137 HEJ 0.415385 0.804598
138 ATP 0.415385 0.804598
139 AP5 0.414062 0.784091
140 B4P 0.414062 0.784091
141 AR6 0.412214 0.804598
142 AQP 0.412214 0.804598
143 2A5 0.412214 0.827586
144 APR 0.412214 0.804598
145 5FA 0.412214 0.804598
146 BIS 0.411348 0.8
147 AN2 0.410853 0.795455
148 5AL 0.410448 0.816092
149 M33 0.407692 0.795455
150 ATF 0.407407 0.777778
151 9X8 0.407143 0.788889
152 A A A 0.407143 0.795455
153 OMR 0.406667 0.897727
154 8QN 0.405797 0.816092
155 SRP 0.404412 0.83908
156 WAQ 0.404255 0.862069
157 ANP 0.402985 0.786517
158 ADQ 0.402878 0.806818
159 NB8 0.401408 0.811111
160 1ZZ 0.401408 0.886364
161 APU 0.401316 0.769231
162 NJP 0.4 0.788889
163 AHX 0.4 0.811111
164 AT4 0.4 0.777778
Ligand no: 2; Ligand: SCD; Similar ligands found: 153
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 COS 0.81746 0.954545
11 CAO 0.81746 0.94382
12 30N 0.81746 0.893617
13 CA6 0.813953 0.865979
14 SCA 0.810606 0.977012
15 CMC 0.807692 0.977012
16 NMX 0.807692 0.903226
17 ETB 0.806452 0.920455
18 FCX 0.804688 0.965909
19 ACO 0.804688 0.94382
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 3KK 0.792308 0.954545
27 FYN 0.792308 0.976744
28 FAM 0.790698 0.954545
29 SOP 0.78626 0.954545
30 COK 0.78626 0.954545
31 A1S 0.781955 0.954545
32 1VU 0.780303 0.94382
33 CA8 0.777778 0.865979
34 2KQ 0.777778 0.955056
35 HGG 0.777778 0.977012
36 MCA 0.776119 0.965909
37 2MC 0.774436 0.913043
38 MC4 0.77037 0.903226
39 2CP 0.77037 0.965909
40 1HE 0.768657 0.933333
41 IVC 0.768657 0.965517
42 3HC 0.768657 0.965517
43 BCO 0.768657 0.954545
44 1CZ 0.768116 0.965909
45 COF 0.764706 0.933333
46 COO 0.762963 0.954545
47 CAA 0.762963 0.965517
48 TGC 0.76087 0.965909
49 BCA 0.759124 0.94382
50 CIC 0.755396 0.977012
51 HXC 0.753623 0.933333
52 1GZ 0.751825 0.94382
53 COW 0.751825 0.94382
54 IRC 0.751825 0.965517
55 BYC 0.751825 0.954545
56 1CV 0.751773 0.977012
57 YE1 0.75 0.965517
58 UOQ 0.746479 0.933333
59 NHM 0.746479 0.933333
60 NHW 0.746479 0.933333
61 FAQ 0.746377 0.954545
62 4CA 0.746377 0.94382
63 CO8 0.742857 0.933333
64 5F9 0.737589 0.933333
65 DCC 0.737589 0.933333
66 MFK 0.737589 0.933333
67 MYA 0.737589 0.933333
68 ST9 0.737589 0.933333
69 UCC 0.737589 0.933333
70 0ET 0.732394 0.933333
71 2NE 0.730496 0.933333
72 S0N 0.730496 0.977012
73 CS8 0.727273 0.923077
74 4CO 0.725352 0.94382
75 0FQ 0.725352 0.954545
76 HDC 0.722222 0.933333
77 01A 0.72028 0.913043
78 MRS 0.717241 0.933333
79 MRR 0.717241 0.933333
80 WCA 0.715278 0.933333
81 YNC 0.712329 0.94382
82 4KX 0.710345 0.923077
83 NHQ 0.709459 0.965517
84 8Z2 0.707483 0.923077
85 HFQ 0.705479 0.933333
86 DAK 0.70068 0.923077
87 01K 0.695364 0.954545
88 1HA 0.677632 0.933333
89 CA3 0.670968 0.954545
90 F8G 0.668831 0.913979
91 COT 0.668831 0.954545
92 COD 0.666667 0.965116
93 CCQ 0.659864 0.913043
94 93P 0.65625 0.965909
95 7L1 0.654676 0.94382
96 93M 0.646341 0.965909
97 UCA 0.645963 0.933333
98 CA5 0.639752 0.913043
99 CO7 0.630137 0.954545
100 OXT 0.597701 0.893617
101 JBT 0.583333 0.894737
102 4BN 0.581921 0.893617
103 5TW 0.581921 0.893617
104 BSJ 0.577143 0.944444
105 HMG 0.564103 0.943182
106 COA PLM 0.556962 0.901099
107 PLM COA 0.556962 0.901099
108 PAP 0.553719 0.811765
109 ASP ASP ASP ILE CMC NH2 0.532164 0.932584
110 A3P 0.504132 0.8
111 PPS 0.503937 0.734043
112 ACE SER ASP ALY THR NH2 COA 0.497297 0.932584
113 0WD 0.486486 0.788889
114 191 0.478261 0.846939
115 RFC 0.470588 0.933333
116 SFC 0.470588 0.933333
117 PTJ 0.446043 0.894118
118 3AM 0.442623 0.788235
119 A22 0.433824 0.813953
120 PUA 0.433121 0.820225
121 WAQ 0.428571 0.882353
122 A2D 0.428571 0.802326
123 PAJ 0.427536 0.905882
124 YLB 0.426667 0.930233
125 48N 0.425676 0.829545
126 3OD 0.425532 0.847059
127 AGS 0.424242 0.786517
128 ATR 0.424242 0.8
129 SAP 0.424242 0.786517
130 F2R 0.422078 0.886364
131 NJP 0.422078 0.806818
132 ADP 0.418605 0.823529
133 YLP 0.416107 0.908046
134 A2R 0.416058 0.835294
135 NA7 0.411348 0.858824
136 OAD 0.411348 0.847059
137 BA3 0.410853 0.802326
138 HEJ 0.409091 0.823529
139 ATP 0.409091 0.823529
140 SRP 0.408759 0.858824
141 AP5 0.407692 0.802326
142 B4P 0.407692 0.802326
143 5FA 0.406015 0.823529
144 AQP 0.406015 0.823529
145 AR6 0.406015 0.823529
146 APR 0.406015 0.823529
147 2A5 0.406015 0.847059
148 1ZZ 0.405594 0.863636
149 AN2 0.40458 0.813953
150 DLL 0.404255 0.813953
151 M33 0.401515 0.813953
152 9X8 0.401408 0.806818
153 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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