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Receptor
PDB id Resolution Class Description Source Keywords
2REQ 2.5 Å EC: 5.4.99.2 METHYLMALONYL-COA MUTASE, NON-PRODUCTIVE COA COMPLEX, IN OPE CONFORMATION REPRESENTING SUBSTRATE-FREE STATE PROPIONIBACTERIUM FREUDENREICHII SUBSPSHERMANII ISOMERASE MUTASE INTRAMOLECULAR TRANSFERASE
Ref.: CONFORMATIONAL CHANGES ON SUBSTRATE BINDING TO METH COA MUTASE AND NEW INSIGHTS INTO THE FREE RADICAL M STRUCTURE V. 6 711 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
B12 A:800;
C:800;
Part of Protein;
Part of Protein;
none;
none;
submit data
1330.36 C62 H89 Co N13 O14 P Cc1cc...
COA A:801;
C:801;
Valid;
Valid;
none;
none;
submit data
767.534 C21 H36 N7 O16 P3 S 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: COA; Similar ligands found: 211
No: Ligand ECFP6 Tc MDL keys Tc
1 COA 1 1
2 0T1 0.894737 0.976744
3 DCA 0.893805 0.954023
4 COS 0.887931 0.977012
5 ETB 0.877193 0.920455
6 AMX 0.871795 0.988235
7 30N 0.871795 0.913979
8 CAO 0.871795 0.965909
9 CMX 0.864407 0.976744
10 SCO 0.864407 0.976744
11 ACO 0.857143 0.965909
12 FCX 0.857143 0.94382
13 FAM 0.857143 0.954545
14 HAX 0.85 0.954545
15 3KK 0.842975 0.977012
16 FYN 0.842975 1
17 SOP 0.836066 0.977012
18 MCD 0.836066 0.954545
19 OXK 0.836066 0.977012
20 CA6 0.836066 0.885417
21 COK 0.836066 0.977012
22 CO6 0.829268 0.977012
23 NMX 0.829268 0.903226
24 1VU 0.829268 0.965909
25 CMC 0.829268 0.977012
26 CAJ 0.822581 0.954545
27 SCD 0.822581 0.976744
28 2MC 0.822581 0.934066
29 2CP 0.81746 0.965909
30 A1S 0.816 0.977012
31 3HC 0.816 0.988372
32 IVC 0.816 0.988372
33 1HE 0.816 0.955056
34 MLC 0.816 0.977012
35 BCO 0.816 0.977012
36 COD 0.810345 0.988235
37 COO 0.809524 0.977012
38 MCA 0.809524 0.965909
39 CAA 0.809524 0.988372
40 YE1 0.809524 0.965517
41 MC4 0.80315 0.923913
42 SCA 0.80315 0.977012
43 CA8 0.796875 0.885417
44 COF 0.796875 0.955056
45 BYC 0.796875 0.977012
46 COW 0.796875 0.965909
47 3CP 0.796875 0.977012
48 IRC 0.796875 0.988372
49 1GZ 0.796875 0.965909
50 HGG 0.796875 0.977012
51 2KQ 0.796875 0.955056
52 BCA 0.790698 0.965909
53 4CA 0.790698 0.965909
54 FAQ 0.790698 0.977012
55 HXC 0.784615 0.955056
56 GRA 0.784615 0.977012
57 1CV 0.781955 0.977012
58 TGC 0.778626 0.965909
59 2NE 0.772727 0.955056
60 1CZ 0.772727 0.965909
61 CO8 0.772727 0.955056
62 S0N 0.772727 0.954545
63 CIC 0.772727 0.977012
64 DCC 0.766917 0.955056
65 UCC 0.766917 0.955056
66 0FQ 0.766917 0.977012
67 MYA 0.766917 0.955056
68 ST9 0.766917 0.955056
69 4CO 0.766917 0.965909
70 5F9 0.766917 0.955056
71 MFK 0.766917 0.955056
72 01A 0.761194 0.934066
73 0ET 0.761194 0.955056
74 WCA 0.755556 0.955056
75 CS8 0.755556 0.944444
76 UOQ 0.75 0.955056
77 NHW 0.75 0.955056
78 NHM 0.75 0.955056
79 4KX 0.75 0.944444
80 HDC 0.75 0.955056
81 MRR 0.744526 0.955056
82 MRS 0.744526 0.955056
83 HFQ 0.744526 0.955056
84 YNC 0.73913 0.965909
85 DAK 0.73913 0.944444
86 8Z2 0.733813 0.944444
87 NHQ 0.723404 0.988372
88 F8G 0.715278 0.913979
89 1HA 0.713287 0.955056
90 01K 0.708333 0.977012
91 COT 0.703448 0.977012
92 CCQ 0.695652 0.934066
93 CA3 0.693878 0.977012
94 7L1 0.692308 0.965909
95 CA5 0.671053 0.934066
96 UCA 0.666667 0.955056
97 93P 0.666667 0.965909
98 CO7 0.664234 0.977012
99 93M 0.64557 0.965909
100 OXT 0.634146 0.913979
101 5TW 0.607143 0.913979
102 4BN 0.607143 0.913979
103 PAP 0.603604 0.811765
104 JBT 0.598837 0.894737
105 BSJ 0.592814 0.944444
106 HMG 0.581081 0.943182
107 COA PLM 0.573333 0.922222
108 PLM COA 0.573333 0.922222
109 A3P 0.54955 0.8
110 PPS 0.547009 0.752688
111 ASP ASP ASP ILE CMC NH2 0.536585 0.932584
112 0WD 0.521739 0.788889
113 SFC 0.490683 0.955056
114 RFC 0.490683 0.955056
115 191 0.490196 0.865979
116 ACE SER ASP ALY THR NH2 COA 0.483333 0.932584
117 3AM 0.482143 0.788235
118 PTJ 0.48062 0.872093
119 4PS 0.477477 0.682353
120 A22 0.468254 0.813953
121 A2D 0.465517 0.802326
122 PUA 0.462585 0.820225
123 PAJ 0.460938 0.883721
124 ATR 0.459016 0.8
125 SAP 0.459016 0.806818
126 AGS 0.459016 0.806818
127 3OD 0.458015 0.825581
128 ADP 0.453782 0.823529
129 A2R 0.448819 0.813953
130 BA3 0.445378 0.802326
131 OAD 0.442748 0.825581
132 NA7 0.442748 0.858824
133 ATP 0.442623 0.823529
134 HEJ 0.442623 0.823529
135 AP5 0.441667 0.802326
136 B4P 0.441667 0.802326
137 AR6 0.439024 0.802326
138 APR 0.439024 0.802326
139 2A5 0.439024 0.847059
140 5FA 0.439024 0.823529
141 AQP 0.439024 0.823529
142 AN2 0.438017 0.813953
143 AT4 0.438017 0.816092
144 48N 0.435714 0.808989
145 M33 0.434426 0.813953
146 9X8 0.431818 0.806818
147 SRP 0.429688 0.837209
148 ANP 0.428571 0.804598
149 ADQ 0.427481 0.804598
150 YLB 0.426573 0.908046
151 YLP 0.425532 0.886364
152 5AL 0.425197 0.813953
153 7D3 0.425 0.793103
154 AD9 0.424 0.804598
155 APU 0.423611 0.786517
156 7D4 0.422764 0.793103
157 CA0 0.422764 0.804598
158 25L 0.422222 0.813953
159 ATF 0.421875 0.795455
160 F2R 0.421769 0.865169
161 NJP 0.421769 0.806818
162 A2P 0.421488 0.788235
163 A A A 0.421053 0.813953
164 8QN 0.419847 0.813953
165 PNS 0.419643 0.682353
166 ACP 0.419355 0.825581
167 NDP 0.417808 0.788889
168 ACQ 0.417323 0.825581
169 A1R 0.416667 0.882353
170 ATP A A A 0.416058 0.770115
171 A 0.415254 0.8
172 AMP 0.415254 0.8
173 1ZZ 0.414815 0.842697
174 NB8 0.414815 0.808989
175 TXA 0.414815 0.816092
176 FYA 0.414815 0.813953
177 DLL 0.413534 0.793103
178 00A 0.413534 0.758242
179 AHX 0.413534 0.829545
180 PAX 0.412903 0.793478
181 DQV 0.411348 0.813953
182 OMR 0.409722 0.853933
183 9ZD 0.409091 0.818182
184 25A 0.409091 0.802326
185 OOB 0.409091 0.793103
186 9ZA 0.409091 0.818182
187 NPW 0.408163 0.822222
188 6YZ 0.407692 0.825581
189 A A 0.407407 0.781609
190 WAQ 0.407407 0.860465
191 TAT 0.40625 0.816092
192 T99 0.40625 0.816092
193 AMO 0.406015 0.837209
194 4AD 0.406015 0.827586
195 A3R 0.406015 0.882353
196 FA5 0.405797 0.816092
197 YAP 0.405797 0.806818
198 B5Y 0.405797 0.786517
199 TXP 0.405405 0.829545
200 ABM 0.404959 0.781609
201 PRX 0.404762 0.825581
202 ME8 0.404412 0.842697
203 BIS 0.404412 0.818182
204 AFH 0.404255 0.78022
205 J7V 0.403846 0.778947
206 NAI 0.402778 0.777778
207 ODP 0.402685 0.78022
208 DAL AMP 0.401515 0.793103
209 AU1 0.4 0.804598
210 ADX 0.4 0.752688
211 SRA 0.4 0.784091
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: 183
This union binding pocket(no: 1) in the query (biounit: 1req.bio2) has 43 residues
No: Leader PDB Ligand Sequence Similarity
1 1SR9 KIV 1.72684
2 4RF7 ARG 2.04082
3 3O2K DST 2.1097
4 3B6R ADP 2.3622
5 1DJX I3P 2.40385
6 1OFZ FUL 2.5641
7 1OFZ FUC 2.5641
8 4RD0 GDP 2.6506
9 1M3U KPL 2.65152
10 4KCT PYR 2.80561
11 1U6R ADP 2.89474
12 1G51 AMP 2.93103
13 4S28 AIR 2.95139
14 4S28 SAH 2.95139
15 2JBM SRT 3.01003
16 4B0T ADP 3.24544
17 3GD9 GLC BGC BGC BGC 3.26975
18 5T9C G3P 3.35821
19 2ICK DMA 3.43348
20 3GJB AKG 3.44828
21 2VEG PMM 3.45369
22 5MRH Q9Z 3.45369
23 4FXQ G9L 3.47826
24 1O68 KIV 3.63636
25 4RW3 IPD 3.64238
26 5L2R MLA 3.64238
27 3B1Q NOS 3.68098
28 3H22 B53 3.7037
29 2CIR BG6 3.7037
30 1F9V ADP 3.7464
31 3A16 PXO 3.75335
32 5H9Y BGC BGC BGC BGC 3.82883
33 3UWV 2PG 3.83142
34 3P7N FMN 3.87597
35 1VMK GUN 3.97112
36 3U6W KIV 3.98126
37 3H55 GLA 4
38 2J5B TYE 4.02299
39 2XG5 EC5 4.04624
40 2XG5 EC2 4.04624
41 5F7J ADE 4.0625
42 4D4U FUC GAL 4.12698
43 4D4U FUC GAL NAG 4.12698
44 4D52 GXL 4.12698
45 4D52 GIV 4.12698
46 1VJ7 GPX 4.3257
47 4YJK URA 4.36508
48 5EJL C2E 4.43548
49 6CZI 38E 4.46429
50 4NZF ARB 4.46429
51 2R5V HHH 4.48179
52 2BHZ MAL 4.48505
53 6EK3 OUL 4.52489
54 1EYE PMM 4.64286
55 4HWT 1B2 4.84262
56 4V3C C 4.89691
57 5GLT BGC GAL NAG GAL 4.92958
58 4H6B 10Y 5.12821
59 4H6B 10X 5.12821
60 1H8S AIC 5.15873
61 3MI3 LYS 5.20095
62 5M77 7K2 7K3 5.26316
63 5VJE GOS 5.30726
64 5AB1 BCD TA5 HP6 MAN 5.33333
65 1GPM AMP 5.33333
66 4RT1 C2E 5.35714
67 3PGU OLA 5.38642
68 1SDW IYT 5.41401
69 2IUW AKG 5.46218
70 2IGA XXP 5.47945
71 1VRP ADP 5.51181
72 2GVJ DGB 5.70265
73 2OJW ADP 5.72917
74 2Y5S 78H 5.78231
75 4JH6 FCN 5.7971
76 2G30 ALA ALA PHE 5.81395
77 1NKI PPF 5.92593
78 4J0M BLD 5.96546
79 1OPB RET 5.97015
80 3KYF 5GP 5GP 6.06061
81 5J75 6GQ 6.06061
82 5EO8 TFU 6.10932
83 1I06 TZL 6.11111
84 4XDA RIB 6.14887
85 1MJJ HAL 6.1674
86 1F52 ADP 6.19658
87 5V3D FCN 6.2069
88 5KJW 53C 6.32318
89 5I0U DCY 6.5
90 5YSI NCA 6.57895
91 5FPE 3TR 6.71835
92 3V8S 0HD 6.82927
93 1MH5 HAL 6.84932
94 3T7V MD0 6.85714
95 4WOE ADP 6.90738
96 5N0L ILE 6.91824
97 3CBC DBS 7.07071
98 3BJE URA 7.16332
99 1Y9Q MED 7.29167
100 3UXL CFI 7.31071
101 2A5F NAD 7.42857
102 3LGS ADE 7.49064
103 3LGS SAH 7.49064
104 1EX7 5GP 7.52688
105 1GT4 UNA 7.54717
106 4BG4 ADP 7.58427
107 4LIT AKG 7.61671
108 1M5W DXP 7.81893
109 2GOO NDG 7.84314
110 5OCG 9R5 7.93651
111 5NBW 8SK 8.10811
112 4IF4 BEF 8.17308
113 5BTX CMP 8.21918
114 1DZK PRZ 8.28025
115 4RYV ZEA 8.3871
116 5DYO FLU 8.49057
117 3H0L ADP 8.51064
118 3THR C2F 8.53242
119 1X9I G6Q 8.60927
120 5YRV 5AD 8.66426
121 6FA4 D1W 8.67052
122 2Z3U CRR 8.70588
123 2Y7P SAL 8.7156
124 5GP0 GPP 8.72483
125 5LUN OGA 8.80682
126 4JN6 OXL 8.82353
127 4P7U 1PS 8.92857
128 2C49 ADN 8.9404
129 2P7Q GG6 9.02256
130 1KTC NGA 9.1358
131 2ZSC BTN 9.21986
132 1J3R 6PG 9.47368
133 5YJS SAL 9.48718
134 2ZMF CMP 9.52381
135 5F6U 5VK 9.55414
136 4Y24 TD2 9.74026
137 2C3W GLC GLC GLC GLC 9.80392
138 2E27 AB0 10.084
139 1ZOT EMA 10.1449
140 3ZGJ RMN 10.2426
141 6GNO XDI 10.3704
142 4B5W PYR 10.5469
143 3SAO DBH 10.625
144 3SAO NKN 10.625
145 2VDF OCT 10.6719
146 5H9P TD2 10.7595
147 4FK7 P34 10.917
148 5Y4R C2E 11.0345
149 5W75 SUC 11.2245
150 5XEG AKG 11.2554
151 4OCT AKG 11.2613
152 6BU0 IHP 11.4504
153 3ZW0 FUC 11.4943
154 3ZW2 GAL FUC 11.4943
155 3ZW2 NAG GAL FUC 11.4943
156 1ZNY GDP 11.5942
157 3WG3 A2G GAL NAG FUC 11.7978
158 1Y7P RIP 12.5561
159 3JQ3 ADP 12.8415
160 1WW5 SGA BGC 13.125
161 6F7X MFU 13.3333
162 2BS5 BGC GAL FUC 13.3333
163 6CLV 6MB 13.4021
164 3ESS 18N 13.4783
165 1P0Z FLC 13.7405
166 3ZO7 K6H 13.8298
167 3NZ1 3NY 14.1762
168 2YKL NLD 14.3519
169 4B1M FRU FRU 15.1351
170 5XQW 8EU 15.2074
171 2YIP YIO 15.942
172 1IIU RTL 16.092
173 4COQ SAN 16.1943
174 4B1L FRU 16.9697
175 4CSD MFU 17.2794
176 2RDE C2E 17.9283
177 3M3E GAL A2G NPO 18.0124
178 2FKA BEF 18.6047
179 2TPI ILE VAL 18.7773
180 1UGY GLA BGC 20
181 4BJ8 BTN 20.6349
182 2BOS GLA GAL 29.4118
183 4M1U A2G MBG 30
Pocket No.: 2; Query (leader) PDB : 1REQ; Ligand: DCA; Similar sites found with APoc: 30
This union binding pocket(no: 2) in the query (biounit: 1req.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 1OFL NGK GCD 1.8711
3 2VQ5 HBA 2.98507
4 4IP7 FLC 3.13075
5 3JU6 ANP 3.24324
6 1S5O 152 3.57143
7 1ELI PYC 3.59897
8 5INJ 6C7 4.19753
9 5VZ0 ADP 4.23862
10 2BMB PMM 4.40367
11 6BYM HC3 4.4335
12 3GM5 CIT 5.03145
13 1GPM CIT 5.33333
14 2CI5 HCS 5.6338
15 1NVM OXL 6.08974
16 6G9I CXX 6.66667
17 1VKF CIT 6.91489
18 5N0F 7K2 7.45856
19 1USF NAP 7.86517
20 1F5F DHT 9.26829
21 4EE7 PIS 9.53947
22 3HP8 SUC 10
23 5KY9 GDP 11.5493
24 1QD1 FON 12
25 2VFT SOR 12.0853
26 1L5Y BEF 13.5484
27 2OMN IPH 14.7465
28 5KEW 6SB 15.9574
29 6BR7 BEF 20.3008
30 1RZX ACE VAL LYS GLU SER LEU VAL 20.4082
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