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 (2D)
Ligand no: 1; Ligand: MCD; Similar ligands found: 194
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 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 SOP 0.79845 0.955056
24 OXK 0.79845 0.955056
25 KGP 0.79845 0.867347
26 YZS 0.79845 0.867347
27 A1S 0.793893 0.955056
28 CO6 0.792308 0.955056
29 FYN 0.790698 0.954545
30 3KK 0.790698 0.955056
31 3CP 0.789474 0.955056
32 CA8 0.789474 0.848485
33 COK 0.784615 0.933333
34 SCA 0.781955 0.955056
35 MLC 0.780303 0.955056
36 IVC 0.780303 0.94382
37 3HC 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 BCO 0.766917 0.933333
46 KGJ 0.766917 0.894737
47 1HE 0.766917 0.934066
48 GRA 0.764706 0.955056
49 2KQ 0.762963 0.977528
50 IRC 0.762963 0.94382
51 HGG 0.762963 0.955056
52 COO 0.761194 0.933333
53 YE1 0.761194 0.94382
54 CAA 0.761194 0.94382
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 BYC 0.75 0.933333
61 COW 0.75 0.923077
62 KFV 0.75 0.876289
63 1GZ 0.75 0.923077
64 KGA 0.75 0.905263
65 FAQ 0.744526 0.933333
66 BCA 0.744526 0.923077
67 0ET 0.742857 0.955556
68 2NE 0.741007 0.913043
69 CO8 0.741007 0.955556
70 S0N 0.741007 0.955056
71 1CZ 0.741007 0.944444
72 CS8 0.737589 0.945055
73 0FQ 0.735714 0.933333
74 MFK 0.735714 0.955556
75 DCC 0.735714 0.955556
76 ST9 0.735714 0.955556
77 UCC 0.735714 0.955556
78 MYA 0.735714 0.955556
79 4CO 0.735714 0.923077
80 5F9 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 RMW 0.647799 0.913043
108 CA5 0.647799 0.893617
109 N9V 0.635135 0.902174
110 UCA 0.63354 0.955556
111 CO7 0.627586 0.933333
112 COA FLC 0.618705 0.921348
113 OXT 0.604651 0.914894
114 5TW 0.588571 0.914894
115 4BN 0.588571 0.914894
116 JBT 0.581006 0.915789
117 BSJ 0.574713 0.923913
118 BUA COA 0.573333 0.901099
119 6NA COA 0.564935 0.923077
120 PAP 0.563025 0.793103
121 EO3 COA 0.55414 0.923077
122 PLM COA 0.55414 0.923077
123 MYR COA 0.55414 0.923077
124 X90 COA 0.55414 0.923077
125 DAO COA 0.55414 0.923077
126 DCR COA 0.55414 0.923077
127 DKA COA 0.55414 0.923077
128 HMG 0.551282 0.922222
129 ASP ASP ASP ILE NH2 CMC 0.538462 0.912088
130 A3P 0.512605 0.781609
131 PPS 0.512 0.71875
132 ACE SER ASP ALY THR NH2 COA 0.502732 0.933333
133 0WD 0.493151 0.771739
134 SFC 0.48503 0.934066
135 RFC 0.48503 0.934066
136 MET VAL ASN ALA CMC 0.483696 0.912088
137 PTJ 0.463235 0.873563
138 ACE MET LEU GLY PRO NH2 COA 0.459184 0.912088
139 5AD NJS 0.454545 0.893617
140 3AM 0.45 0.770115
141 48N 0.441379 0.831461
142 A22 0.440298 0.795455
143 PUA 0.43871 0.802198
144 F2R 0.437086 0.866667
145 A2D 0.435484 0.784091
146 PAJ 0.433824 0.885057
147 HQG 0.432836 0.816092
148 YLB 0.432432 0.909091
149 3OD 0.431655 0.827586
150 ATR 0.430769 0.781609
151 AGS 0.430769 0.769231
152 QA7 0.42963 0.850575
153 9BG 0.427632 0.771739
154 UBG 0.426901 0.826087
155 ADP 0.425197 0.804598
156 A2R 0.422222 0.816092
157 YLP 0.421769 0.909091
158 TXA 0.421429 0.818182
159 8LE 0.421053 0.850575
160 8LQ 0.419118 0.83908
161 BA3 0.417323 0.784091
162 OAD 0.417266 0.827586
163 NA7 0.417266 0.83908
164 HEJ 0.415385 0.804598
165 ATP 0.415385 0.804598
166 B4P 0.414062 0.784091
167 AP5 0.414062 0.784091
168 2A5 0.412214 0.827586
169 APR 0.412214 0.804598
170 AR6 0.412214 0.804598
171 5FA 0.412214 0.804598
172 AQP 0.412214 0.804598
173 BIS 0.411348 0.8
174 AN2 0.410853 0.795455
175 5AL 0.410448 0.816092
176 JNT 0.410072 0.827586
177 M33 0.407692 0.795455
178 ATF 0.407407 0.777778
179 9X8 0.407143 0.788889
180 OMR 0.406667 0.897727
181 8QN 0.405797 0.816092
182 KG4 0.40458 0.806818
183 8LH 0.404412 0.83908
184 SRP 0.404412 0.83908
185 J4G 0.404255 0.850575
186 WAQ 0.404255 0.862069
187 ANP 0.402985 0.786517
188 ADQ 0.402878 0.806818
189 1ZZ 0.401408 0.886364
190 NB8 0.401408 0.811111
191 APU 0.401316 0.769231
192 NJP 0.4 0.788889
193 AT4 0.4 0.777778
194 AHX 0.4 0.811111
Ligand no: 2; Ligand: SCD; Similar ligands found: 182
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 30N 0.81746 0.893617
12 CAO 0.81746 0.94382
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 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 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 2CP 0.77037 0.965909
41 MC4 0.77037 0.903226
42 BCO 0.768657 0.954545
43 1HE 0.768657 0.933333
44 IVC 0.768657 0.965517
45 3HC 0.768657 0.965517
46 KGJ 0.768657 0.893617
47 1CZ 0.768116 0.965909
48 KFV 0.764706 0.875
49 COF 0.764706 0.933333
50 CAA 0.762963 0.965517
51 COO 0.762963 0.954545
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 IRC 0.751825 0.965517
61 COW 0.751825 0.94382
62 1GZ 0.751825 0.94382
63 1CV 0.751773 0.977012
64 SO5 0.75 0.876289
65 LCV 0.75 0.876289
66 YE1 0.75 0.965517
67 NHW 0.746479 0.933333
68 NHM 0.746479 0.933333
69 UOQ 0.746479 0.933333
70 FAQ 0.746377 0.954545
71 4CA 0.746377 0.94382
72 CO8 0.742857 0.933333
73 UCC 0.737589 0.933333
74 DCC 0.737589 0.933333
75 MFK 0.737589 0.933333
76 ST9 0.737589 0.933333
77 MYA 0.737589 0.933333
78 5F9 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 0FQ 0.725352 0.954545
84 4CO 0.725352 0.94382
85 HDC 0.722222 0.933333
86 01A 0.72028 0.913043
87 MRS 0.717241 0.933333
88 MRR 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 DAK 0.70068 0.923077
96 J5H 0.70068 0.954545
97 01K 0.695364 0.954545
98 1HA 0.677632 0.933333
99 CA3 0.670968 0.954545
100 F8G 0.668831 0.913979
101 COT 0.668831 0.954545
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 RMW 0.65 0.933333
107 93M 0.646341 0.965909
108 UCA 0.645963 0.933333
109 CA5 0.639752 0.913043
110 CO7 0.630137 0.954545
111 N9V 0.626667 0.922222
112 COA FLC 0.609929 0.942529
113 OXT 0.597701 0.893617
114 JBT 0.583333 0.894737
115 4BN 0.581921 0.893617
116 5TW 0.581921 0.893617
117 BSJ 0.577143 0.944444
118 BUA COA 0.576159 0.921348
119 6NA COA 0.567742 0.901099
120 HMG 0.564103 0.943182
121 DAO COA 0.556962 0.901099
122 X90 COA 0.556962 0.901099
123 DCR COA 0.556962 0.901099
124 PLM COA 0.556962 0.901099
125 MYR COA 0.556962 0.901099
126 EO3 COA 0.556962 0.901099
127 DKA COA 0.556962 0.901099
128 PAP 0.553719 0.811765
129 ASP ASP ASP ILE NH2 CMC 0.532164 0.932584
130 A3P 0.504132 0.8
131 PPS 0.503937 0.734043
132 ACE SER ASP ALY THR NH2 COA 0.497297 0.932584
133 0WD 0.486486 0.788889
134 SFC 0.470588 0.933333
135 RFC 0.470588 0.933333
136 MET VAL ASN ALA CMC 0.462766 0.911111
137 5AD NJS 0.457627 0.913043
138 PTJ 0.446043 0.894118
139 3AM 0.442623 0.788235
140 A22 0.433824 0.813953
141 PUA 0.433121 0.820225
142 ACE MET LEU GLY PRO NH2 COA 0.432836 0.911111
143 WAQ 0.428571 0.882353
144 A2D 0.428571 0.802326
145 PAJ 0.427536 0.905882
146 YLB 0.426667 0.930233
147 HQG 0.426471 0.835294
148 48N 0.425676 0.829545
149 3OD 0.425532 0.847059
150 ATR 0.424242 0.8
151 AGS 0.424242 0.786517
152 F2R 0.422078 0.886364
153 9BG 0.422078 0.788889
154 NJP 0.422078 0.806818
155 UBG 0.421965 0.844444
156 ADP 0.418605 0.823529
157 J4G 0.41844 0.870588
158 YLP 0.416107 0.908046
159 A2R 0.416058 0.835294
160 8LE 0.414815 0.870588
161 JNT 0.414286 0.847059
162 8LQ 0.413043 0.858824
163 QA7 0.413043 0.870588
164 NA7 0.411348 0.858824
165 OAD 0.411348 0.847059
166 BA3 0.410853 0.802326
167 ATP 0.409091 0.823529
168 HEJ 0.409091 0.823529
169 SRP 0.408759 0.858824
170 AP5 0.407692 0.802326
171 B4P 0.407692 0.802326
172 AQP 0.406015 0.823529
173 2A5 0.406015 0.847059
174 5FA 0.406015 0.823529
175 APR 0.406015 0.823529
176 AR6 0.406015 0.823529
177 1ZZ 0.405594 0.863636
178 AN2 0.40458 0.813953
179 DLL 0.404255 0.813953
180 M33 0.401515 0.813953
181 9X8 0.401408 0.806818
182 LAQ 0.4 0.822222
Similar Ligands (3D)
Ligand no: 1; Ligand: MCD; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: SCD; Similar ligands found: 0
No: Ligand Similarity coefficient
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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