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: 215
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 COS 0.87069 0.932584
7 CAO 0.87069 0.922222
8 30N 0.87069 0.873684
9 CMX 0.863248 0.954023
10 SCO 0.863248 0.954023
11 ACO 0.855932 0.94382
12 FCX 0.855932 0.922222
13 FAM 0.855932 0.932584
14 HAX 0.84874 0.932584
15 1VU 0.842975 0.965909
16 3KK 0.841667 0.954545
17 FYN 0.841667 0.954023
18 CAJ 0.836066 0.977012
19 MCD 0.834711 0.954545
20 CA6 0.834711 0.865979
21 COK 0.834711 0.932584
22 SOP 0.834711 0.954545
23 OXK 0.834711 0.932584
24 3HC 0.829268 0.943182
25 IVC 0.829268 0.943182
26 BCO 0.829268 0.954545
27 NMX 0.827869 0.882979
28 CO6 0.827869 0.954545
29 CMC 0.827869 0.932584
30 2MC 0.821138 0.913043
31 SCD 0.821138 0.954023
32 MLC 0.814516 0.932584
33 1HE 0.814516 0.912088
34 A1S 0.814516 0.932584
35 COW 0.809524 0.922222
36 HGG 0.809524 0.932584
37 CA8 0.809524 0.846939
38 BYC 0.809524 0.932584
39 MCA 0.808 0.94382
40 CAA 0.808 0.943182
41 COO 0.808 0.932584
42 YE1 0.808 0.943182
43 FAQ 0.80315 0.932584
44 SCA 0.801587 0.932584
45 2CP 0.801587 0.94382
46 MC4 0.801587 0.903226
47 HXC 0.796875 0.955056
48 3CP 0.795276 0.932584
49 2KQ 0.795276 0.933333
50 IRC 0.795276 0.943182
51 COF 0.795276 0.912088
52 1GZ 0.795276 0.922222
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 MFK 0.778626 0.955056
60 DCC 0.778626 0.955056
61 ST9 0.778626 0.955056
62 0FQ 0.778626 0.932584
63 UCC 0.778626 0.955056
64 MYA 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 NHM 0.761194 0.955056
75 UOQ 0.761194 0.955056
76 01A 0.759399 0.892473
77 MRS 0.755556 0.955056
78 MRR 0.755556 0.955056
79 1CV 0.753731 0.932584
80 WCA 0.753731 0.912088
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 93P 0.675497 0.922222
94 CA5 0.668874 0.892473
95 UCA 0.664474 0.933333
96 CO7 0.661765 0.932584
97 93M 0.653846 0.922222
98 PAP 0.614679 0.811765
99 OXT 0.612121 0.893617
100 4BN 0.60479 0.893617
101 5TW 0.60479 0.893617
102 BSJ 0.6 0.902174
103 JBT 0.587209 0.875
104 COA PLM 0.581081 0.922222
105 PLM COA 0.581081 0.922222
106 COA MYR 0.581081 0.922222
107 HMG 0.578231 0.9
108 A3P 0.559633 0.8
109 PPS 0.556522 0.734043
110 0WD 0.540741 0.788889
111 RFC 0.496855 0.933333
112 SFC 0.496855 0.933333
113 191 0.496689 0.865979
114 3AM 0.490909 0.788235
115 PTJ 0.488189 0.872093
116 PUA 0.479167 0.820225
117 A22 0.475806 0.813953
118 ACE SER ASP ALY THR NH2 COA 0.47541 0.911111
119 A2D 0.473684 0.802326
120 PAJ 0.468254 0.883721
121 SAP 0.466667 0.786517
122 AGS 0.466667 0.786517
123 ATR 0.466667 0.8
124 3OD 0.465116 0.825581
125 ADP 0.461538 0.823529
126 A2R 0.456 0.813953
127 BA3 0.452991 0.802326
128 ATP 0.45 0.823529
129 OAD 0.449612 0.825581
130 NA7 0.449612 0.858824
131 B4P 0.449153 0.802326
132 AP5 0.449153 0.802326
133 2A5 0.446281 0.847059
134 AQP 0.446281 0.823529
135 5FA 0.446281 0.823529
136 AR6 0.446281 0.802326
137 APR 0.446281 0.802326
138 AN2 0.445378 0.813953
139 YLB 0.442857 0.908046
140 YLP 0.442029 0.908046
141 48N 0.442029 0.829545
142 M33 0.441667 0.813953
143 APU 0.439716 0.786517
144 OOB 0.4375 0.793103
145 SRP 0.436508 0.837209
146 ANP 0.435484 0.804598
147 ADQ 0.434109 0.804598
148 NDP 0.433566 0.788889
149 7D3 0.432203 0.793103
150 5AL 0.432 0.813953
151 FYA 0.431818 0.813953
152 AD9 0.430894 0.804598
153 00A 0.430769 0.758242
154 DLL 0.430769 0.793103
155 CA0 0.429752 0.804598
156 7D4 0.429752 0.793103
157 A2P 0.428571 0.788235
158 25L 0.428571 0.813953
159 ATF 0.428571 0.795455
160 NJP 0.427586 0.806818
161 A A A 0.427481 0.813953
162 8QN 0.426357 0.813953
163 ACP 0.42623 0.825581
164 OMR 0.425532 0.875
165 ACQ 0.424 0.825581
166 4AD 0.423077 0.827586
167 PRX 0.422764 0.847059
168 AMP 0.422414 0.8
169 A 0.422414 0.8
170 ATP A A A 0.422222 0.770115
171 FA5 0.422222 0.816092
172 1ZZ 0.421053 0.863636
173 NB8 0.421053 0.808989
174 TXA 0.421053 0.816092
175 AHX 0.419847 0.829545
176 NAI 0.41844 0.777778
177 PAX 0.418301 0.793478
178 3UK 0.416667 0.784091
179 25A 0.415385 0.802326
180 NPW 0.413793 0.822222
181 WAQ 0.413534 0.83908
182 A A 0.413534 0.781609
183 AP0 0.412587 0.769231
184 A1R 0.412214 0.882353
185 AMO 0.412214 0.837209
186 YAP 0.411765 0.806818
187 ABM 0.411765 0.781609
188 TXP 0.410959 0.829545
189 ME8 0.410448 0.822222
190 BIS 0.410448 0.797753
191 AFH 0.410072 0.78022
192 1DG 0.409091 0.788889
193 DG1 0.409091 0.788889
194 ODP 0.408163 0.78022
195 SRA 0.40678 0.764045
196 AU1 0.406504 0.804598
197 ADX 0.406504 0.734043
198 TXE 0.405594 0.818182
199 TYM 0.405594 0.816092
200 XNP 0.405405 0.791209
201 2AM 0.405172 0.8
202 A3G 0.403361 0.764706
203 BEF ADP 0.403226 0.736264
204 50T 0.403226 0.793103
205 A3T 0.403226 0.741176
206 ADP BEF 0.403226 0.736264
207 LAD 0.402985 0.862069
208 YLC 0.402778 0.863636
209 TAT 0.401575 0.795455
210 GAP 0.401575 0.804598
211 NZQ 0.401361 0.8
212 CNA 0.401361 0.816092
213 AYB 0.401361 0.897727
214 52H 0.4 0.75
215 APC 0.4 0.837209
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1REQ; Ligand: DCA; Similar sites found: 110
This union binding pocket(no: 1) in the query (biounit: 1req.bio2) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SR9 KIV 0.03703 0.41767 1.72684
2 3O2K DST 0.03529 0.41864 2.1097
3 3B6R ADP 0.03195 0.4034 2.3622
4 1DJX I3P 0.01347 0.43316 2.40385
5 4AMW 5DI 0.03568 0.4178 2.51177
6 4KCT PYR 0.01732 0.43146 2.80561
7 1U6R ADP 0.01632 0.41459 2.89474
8 1G51 AMP 0.01892 0.43314 2.93103
9 2JBM SRT 0.02914 0.40757 3.01003
10 3GD9 GLC BGC BGC BGC 0.006733 0.44468 3.26975
11 2ICK DMA 0.04848 0.40038 3.43348
12 2VEG PMM 0.03284 0.41641 3.45369
13 5MRH Q9Z 0.047 0.4079 3.45369
14 4FXQ G9L 0.01952 0.4333 3.47826
15 4RW3 IPD 0.008608 0.44783 3.64238
16 3H22 B53 0.0165 0.42105 3.7037
17 2CIR BG6 0.04052 0.41531 3.7037
18 3A16 PXO 0.008536 0.43311 3.75335
19 3P7N FMN 0.0253 0.40245 3.87597
20 3U6W KIV 0.04676 0.41234 3.98126
21 2J5B TYE 0.01526 0.43315 4.02299
22 2XG5 EC2 0.01847 0.41849 4.04624
23 2XG5 EC5 0.01847 0.41849 4.04624
24 5F7J ADE 0.01797 0.43658 4.0625
25 4D4U FUC GAL 0.006684 0.45332 4.12698
26 1VJ7 GPX 0.02018 0.42679 4.3257
27 4NZF ARB 0.04657 0.41188 4.46429
28 2R5V HHH 0.02206 0.41816 4.48179
29 1EYE PMM 0.04825 0.40048 4.64286
30 4HWT 1B2 0.01606 0.41183 4.84262
31 4H6B 10Y 0.04857 0.40362 5.12821
32 4H6B 10X 0.04878 0.40023 5.12821
33 1H8S AIC 0.04661 0.4081 5.15873
34 3MI3 LYS 0.04557 0.41241 5.20095
35 5M77 7K2 7K3 0.042 0.40364 5.26316
36 1ULE GLA GAL NAG 0.03703 0.40385 5.33333
37 3PGU OLA 0.03878 0.40885 5.38642
38 2IUW AKG 0.03832 0.41275 5.46218
39 1VRP ADP 0.01355 0.42536 5.51181
40 5MX4 HPA 0.003481 0.47484 5.5794
41 2GVJ DGB 0.002616 0.44537 5.70265
42 2Y5S 78H 0.02047 0.41984 5.78231
43 4JH6 FCN 0.04625 0.40829 5.7971
44 2G30 ALA ALA PHE 0.0002545 0.47434 5.81395
45 1NKI PPF 0.02064 0.4316 5.92593
46 4J0M BLD 0.04546 0.40184 5.96546
47 1OPB RET 0.02407 0.40348 5.97015
48 3KYF 5GP 5GP 0.03853 0.409 6.06061
49 4XDA RIB 0.02224 0.42166 6.14887
50 1F52 ADP 0.03721 0.40638 6.19658
51 1MH5 HAL 0.01438 0.40031 6.84932
52 3T7V MD0 0.03923 0.41606 6.85714
53 4WOE ADP 0.002542 0.48483 6.90738
54 3CBC DBS 0.04737 0.40265 7.07071
55 3BJE URA 0.01073 0.44767 7.16332
56 1Y9Q MED 0.03979 0.41452 7.29167
57 2A5F NAD 0.04102 0.40099 7.42857
58 1AJ0 PH2 0.03421 0.40192 7.44681
59 3LGS ADE 0.02034 0.43212 7.49064
60 1EX7 5GP 0.03272 0.42047 7.52688
61 4BG4 ADP 0.01161 0.42175 7.58427
62 4LIT AKG 0.01338 0.44346 7.61671
63 4DSU BZI 0.00572 0.46377 7.93651
64 5NBW 8SK 0.03816 0.40581 8.10811
65 4IF4 BEF 0.02331 0.40545 8.17308
66 5BTX CMP 0.01321 0.44182 8.21918
67 1DZK PRZ 0.03563 0.40104 8.28025
68 4RYV ZEA 0.03323 0.41242 8.3871
69 3H0L ADP 0.001742 0.48507 8.51064
70 3THR C2F 0.0244 0.40921 8.53242
71 2Y7P SAL 0.03183 0.42114 8.7156
72 5LUN OGA 0.0355 0.41849 8.80682
73 4JN6 OXL 0.04068 0.40757 8.82353
74 2C49 ADN 0.02927 0.40229 8.9404
75 2P7Q GG6 0.03796 0.41298 9.02256
76 1KTC NGA 0.04686 0.41173 9.1358
77 2ZSC BTN 0.04211 0.40041 9.21986
78 2E27 AB0 0.03862 0.40554 10.084
79 1ZOT EMA 0.04372 0.40607 10.1449
80 3ZGJ RMN 0.01318 0.44238 10.2426
81 3SAO DBH 0.003573 0.47607 10.625
82 3SAO NKN 0.01031 0.43928 10.625
83 2VDF OCT 0.02729 0.44929 10.6719
84 1SN0 T44 0.04515 0.40199 10.7692
85 4FK7 P34 0.001397 0.48442 10.917
86 4OCT AKG 0.02671 0.41745 11.2613
87 3ZW0 FUC 0.0239 0.42758 11.4943
88 3ZW2 GAL FUC 0.02891 0.41208 11.4943
89 3ZW2 NAG GAL FUC 0.02891 0.40873 11.4943
90 1ZNY GDP 0.03085 0.42189 11.5942
91 2WZ5 MET 0.008593 0.42046 11.7647
92 3WG3 A2G GAL NAG FUC 0.02397 0.42823 11.7978
93 1Y7P RIP 0.04882 0.40792 12.5561
94 3JQ3 ADP 0.02765 0.41666 12.8415
95 2BO9 VAL 0.03465 0.41908 13.0631
96 3ESS 18N 0.03622 0.4149 13.4783
97 1P0Z FLC 0.04491 0.41302 13.7405
98 1AD4 HH2 0.01126 0.4294 14.2857
99 2YKL NLD 0.01375 0.42876 14.3519
100 5EWK P34 0.02492 0.42687 14.5
101 4B1M FRU FRU 0.01103 0.44684 15.1351
102 1IIU RTL 0.0173 0.40456 16.092
103 4COQ SAN 0.04524 0.41233 16.1943
104 4B1L FRU 0.01793 0.43023 16.9697
105 4CSD MFU 0.04248 0.41303 17.2794
106 2FKA BEF 0.00589 0.45798 18.6047
107 2TPI ILE VAL 0.03161 0.40066 18.7773
108 1UGY GLA BGC 0.0169 0.42654 20
109 2BOS GLA GAL 0.01159 0.41178 29.4118
110 4M1U A2G MBG 0.01921 0.42148 30
Pocket No.: 2; Query (leader) PDB : 1REQ; Ligand: DCA; Similar sites found: 19
This union binding pocket(no: 2) in the query (biounit: 1req.bio1) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1OFL NGK GCD 0.04801 0.40862 1.8711
2 2VQ5 HBA 0.03195 0.41309 2.98507
3 3JU6 ANP 0.001998 0.48748 3.24324
4 1S5O 152 0.01888 0.43593 3.57143
5 2BMB PMM 0.04802 0.40059 4.40367
6 3GM5 CIT 0.009758 0.44625 5.03145
7 1GPM CIT 0.03822 0.41693 5.33333
8 2CI5 HCS 0.04273 0.40607 5.6338
9 1EPB REA 0.012 0.42444 6.70732
10 1VKF CIT 0.04372 0.41131 6.91489
11 3LGS SAH 0.04835 0.40044 7.49064
12 2ZMF CMP 0.0219 0.40543 9.52381
13 4EE7 PIS 0.009099 0.44111 9.53947
14 5KY9 GDP 0.03746 0.40301 11.5493
15 2VFT SOR 0.02031 0.42375 12.0853
16 2OMN IPH 0.03019 0.40039 14.7465
17 2YIP YIO 0.01138 0.44694 15.942
18 5KEW 6SB 0.04952 0.40666 15.9574
19 1RZX ACE VAL LYS GLU SER LEU VAL 0.03666 0.41943 20.4082
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