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Receptor
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
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...
DCA A:801;
C:801;
Valid;
Valid;
none;
none;
submit data
735.469 C21 H36 N7 O16 P3 CCNC(...
GOL A:802;
A:803;
B:1;
B:639;
B:640;
C:802;
C:803;
D:1;
D:639;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(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: DCA; Similar ligands found: 230
No: Ligand ECFP6 Tc MDL keys Tc
1 DCA 1 1
2 0T1 0.910714 0.976744
3 COA 0.893805 0.954023
4 ETB 0.892857 0.942529
5 AMX 0.87069 0.965116
6 30N 0.87069 0.873684
7 COS 0.87069 0.932584
8 CAO 0.87069 0.922222
9 SCO 0.863248 0.954023
10 CMX 0.863248 0.954023
11 ACO 0.855932 0.94382
12 FAM 0.855932 0.932584
13 FCX 0.855932 0.922222
14 HAX 0.84874 0.932584
15 1VU 0.842975 0.965909
16 FYN 0.841667 0.954023
17 3KK 0.841667 0.954545
18 CAJ 0.836066 0.977012
19 CA6 0.834711 0.865979
20 SOP 0.834711 0.954545
21 OXK 0.834711 0.932584
22 MCD 0.834711 0.954545
23 COK 0.834711 0.932584
24 IVC 0.829268 0.943182
25 BCO 0.829268 0.954545
26 3HC 0.829268 0.943182
27 NMX 0.827869 0.882979
28 CMC 0.827869 0.932584
29 CO6 0.827869 0.954545
30 SCD 0.821138 0.954023
31 2MC 0.821138 0.913043
32 MLC 0.814516 0.932584
33 1HE 0.814516 0.912088
34 A1S 0.814516 0.932584
35 BYC 0.809524 0.932584
36 COW 0.809524 0.922222
37 HGG 0.809524 0.932584
38 CA8 0.809524 0.846939
39 COO 0.808 0.932584
40 CAA 0.808 0.943182
41 MCA 0.808 0.94382
42 YE1 0.808 0.943182
43 FAQ 0.80315 0.932584
44 2CP 0.801587 0.94382
45 MC4 0.801587 0.903226
46 SCA 0.801587 0.932584
47 HXC 0.796875 0.955056
48 3CP 0.795276 0.932584
49 IRC 0.795276 0.943182
50 1GZ 0.795276 0.922222
51 COF 0.795276 0.912088
52 2KQ 0.795276 0.933333
53 4CA 0.789062 0.922222
54 BCA 0.789062 0.922222
55 2NE 0.784615 0.912088
56 S0N 0.784615 0.932584
57 CO8 0.784615 0.955056
58 GRA 0.782946 0.932584
59 DCC 0.778626 0.955056
60 ST9 0.778626 0.955056
61 MYA 0.778626 0.955056
62 0FQ 0.778626 0.932584
63 UCC 0.778626 0.955056
64 MFK 0.778626 0.955056
65 5F9 0.778626 0.955056
66 TGC 0.776923 0.922222
67 0ET 0.772727 0.955056
68 CIC 0.770992 0.932584
69 1CZ 0.770992 0.922222
70 CS8 0.766917 0.944444
71 4CO 0.765152 0.922222
72 HDC 0.761194 0.955056
73 NHW 0.761194 0.955056
74 UOQ 0.761194 0.955056
75 NHM 0.761194 0.955056
76 01A 0.759399 0.892473
77 MRR 0.755556 0.955056
78 MRS 0.755556 0.955056
79 WCA 0.753731 0.912088
80 1CV 0.753731 0.932584
81 4KX 0.748148 0.902174
82 8Z2 0.744526 0.944444
83 HFQ 0.742647 0.912088
84 DAK 0.737226 0.902174
85 YNC 0.737226 0.922222
86 1HA 0.723404 0.912088
87 NHQ 0.721429 0.943182
88 COD 0.719008 0.942529
89 COT 0.713287 0.932584
90 01K 0.706294 0.954545
91 CCQ 0.705882 0.913043
92 CA3 0.703448 0.932584
93 F8G 0.701389 0.893617
94 7L1 0.689922 0.94382
95 93P 0.675497 0.922222
96 CA5 0.668874 0.892473
97 UCA 0.664474 0.933333
98 CO7 0.661765 0.932584
99 93M 0.653846 0.922222
100 PAP 0.614679 0.811765
101 OXT 0.612121 0.893617
102 4BN 0.60479 0.893617
103 5TW 0.60479 0.893617
104 BSJ 0.6 0.902174
105 JBT 0.587209 0.875
106 COA PLM 0.581081 0.922222
107 PLM COA 0.581081 0.922222
108 HMG 0.578231 0.9
109 A3P 0.559633 0.8
110 PPS 0.556522 0.734043
111 ASP ASP ASP ILE CMC NH2 0.54321 0.911111
112 0WD 0.540741 0.788889
113 SFC 0.496855 0.933333
114 RFC 0.496855 0.933333
115 191 0.496689 0.865979
116 3AM 0.490909 0.788235
117 PTJ 0.488189 0.872093
118 ACE SER ASP ALY THR NH2 COA 0.480447 0.911111
119 PUA 0.479167 0.820225
120 A22 0.475806 0.813953
121 A2D 0.473684 0.802326
122 PAJ 0.468254 0.883721
123 AGS 0.466667 0.786517
124 SAP 0.466667 0.786517
125 ATR 0.466667 0.8
126 3OD 0.465116 0.825581
127 ADP 0.461538 0.823529
128 A2R 0.456 0.813953
129 BA3 0.452991 0.802326
130 HEJ 0.45 0.823529
131 ATP 0.45 0.823529
132 OAD 0.449612 0.825581
133 NA7 0.449612 0.858824
134 AP5 0.449153 0.802326
135 B4P 0.449153 0.802326
136 2A5 0.446281 0.847059
137 AQP 0.446281 0.823529
138 AR6 0.446281 0.802326
139 APR 0.446281 0.802326
140 5FA 0.446281 0.823529
141 AN2 0.445378 0.813953
142 YLB 0.442857 0.908046
143 YLP 0.442029 0.908046
144 48N 0.442029 0.829545
145 M33 0.441667 0.813953
146 APU 0.439716 0.786517
147 9X8 0.438462 0.786517
148 OOB 0.4375 0.793103
149 SRP 0.436508 0.837209
150 ANP 0.435484 0.804598
151 ADQ 0.434109 0.804598
152 NDP 0.433566 0.788889
153 AT4 0.433333 0.795455
154 7D3 0.432203 0.793103
155 5AL 0.432 0.813953
156 FYA 0.431818 0.813953
157 AD9 0.430894 0.804598
158 00A 0.430769 0.758242
159 DLL 0.430769 0.793103
160 CA0 0.429752 0.804598
161 7D4 0.429752 0.793103
162 25L 0.428571 0.813953
163 ATF 0.428571 0.795455
164 A2P 0.428571 0.788235
165 NJP 0.427586 0.806818
166 F2R 0.427586 0.844444
167 A A A 0.427481 0.813953
168 8QN 0.426357 0.813953
169 ACP 0.42623 0.825581
170 OMR 0.425532 0.875
171 ACQ 0.424 0.825581
172 4AD 0.423077 0.827586
173 PRX 0.422764 0.847059
174 A 0.422414 0.8
175 AMP 0.422414 0.8
176 ATP A A A 0.422222 0.770115
177 FA5 0.422222 0.816092
178 B5Y 0.422222 0.786517
179 1ZZ 0.421053 0.863636
180 TXA 0.421053 0.816092
181 NB8 0.421053 0.808989
182 AHX 0.419847 0.829545
183 NAI 0.41844 0.777778
184 PAX 0.418301 0.793478
185 DQV 0.417266 0.813953
186 3UK 0.416667 0.784091
187 25A 0.415385 0.802326
188 9ZD 0.415385 0.818182
189 9ZA 0.415385 0.818182
190 6YZ 0.414062 0.825581
191 NPW 0.413793 0.822222
192 B5V 0.413534 0.775281
193 A A 0.413534 0.781609
194 WAQ 0.413534 0.83908
195 AP0 0.412587 0.769231
196 A1R 0.412214 0.882353
197 AMO 0.412214 0.837209
198 A3R 0.412214 0.882353
199 ABM 0.411765 0.781609
200 YAP 0.411765 0.806818
201 TXP 0.410959 0.829545
202 ME8 0.410448 0.822222
203 BIS 0.410448 0.797753
204 AFH 0.410072 0.78022
205 DG1 0.409091 0.788889
206 1DG 0.409091 0.788889
207 ODP 0.408163 0.78022
208 DAL AMP 0.407692 0.793103
209 SRA 0.40678 0.764045
210 AU1 0.406504 0.804598
211 ADX 0.406504 0.734043
212 TXE 0.405594 0.818182
213 TYM 0.405594 0.816092
214 XNP 0.405405 0.791209
215 2AM 0.405172 0.8
216 A3G 0.403361 0.764706
217 A3T 0.403226 0.741176
218 50T 0.403226 0.793103
219 LAD 0.402985 0.862069
220 YLC 0.402778 0.863636
221 TAT 0.401575 0.795455
222 T99 0.401575 0.795455
223 GAP 0.401575 0.804598
224 B5M 0.40146 0.786517
225 AYB 0.401361 0.897727
226 NZQ 0.401361 0.8
227 CNA 0.401361 0.816092
228 52H 0.4 0.75
229 APC 0.4 0.837209
230 ARG AMP 0.4 0.813187
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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