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: 197
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 CAO 0.871795 0.965909
7 AMX 0.871795 0.988235
8 30N 0.871795 0.913979
9 CMX 0.864407 0.976744
10 SCO 0.864407 0.976744
11 FAM 0.857143 0.954545
12 ACO 0.857143 0.965909
13 FCX 0.857143 0.94382
14 HAX 0.85 0.954545
15 3KK 0.842975 0.977012
16 FYN 0.842975 1
17 CA6 0.836066 0.885417
18 SOP 0.836066 0.977012
19 MCD 0.836066 0.954545
20 COK 0.836066 0.977012
21 OXK 0.836066 0.977012
22 NMX 0.829268 0.903226
23 CO6 0.829268 0.977012
24 CMC 0.829268 0.977012
25 1VU 0.829268 0.965909
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 BCO 0.816 0.977012
31 3HC 0.816 0.988372
32 1HE 0.816 0.955056
33 MLC 0.816 0.977012
34 A1S 0.816 0.977012
35 IVC 0.816 0.988372
36 COD 0.810345 0.988235
37 CAA 0.809524 0.988372
38 COO 0.809524 0.977012
39 MCA 0.809524 0.965909
40 YE1 0.809524 0.965517
41 SCA 0.80315 0.977012
42 MC4 0.80315 0.923913
43 IRC 0.796875 0.988372
44 3CP 0.796875 0.977012
45 CA8 0.796875 0.885417
46 BYC 0.796875 0.977012
47 COW 0.796875 0.965909
48 2KQ 0.796875 0.955056
49 COF 0.796875 0.955056
50 HGG 0.796875 0.977012
51 1GZ 0.796875 0.965909
52 4CA 0.790698 0.965909
53 FAQ 0.790698 0.977012
54 BCA 0.790698 0.965909
55 GRA 0.784615 0.977012
56 HXC 0.784615 0.955056
57 1CV 0.781955 0.977012
58 TGC 0.778626 0.965909
59 1CZ 0.772727 0.965909
60 CO8 0.772727 0.955056
61 S0N 0.772727 0.954545
62 2NE 0.772727 0.955056
63 CIC 0.772727 0.977012
64 0FQ 0.766917 0.977012
65 ST9 0.766917 0.955056
66 4CO 0.766917 0.965909
67 UCC 0.766917 0.955056
68 MFK 0.766917 0.955056
69 DCC 0.766917 0.955056
70 MYA 0.766917 0.955056
71 5F9 0.766917 0.955056
72 01A 0.761194 0.934066
73 0ET 0.761194 0.955056
74 CS8 0.755556 0.944444
75 WCA 0.755556 0.955056
76 4KX 0.75 0.944444
77 UOQ 0.75 0.955056
78 NHW 0.75 0.955056
79 HDC 0.75 0.955056
80 NHM 0.75 0.955056
81 HFQ 0.744526 0.955056
82 MRS 0.744526 0.955056
83 MRR 0.744526 0.955056
84 DAK 0.73913 0.944444
85 YNC 0.73913 0.965909
86 8Z2 0.733813 0.944444
87 NHQ 0.723404 0.988372
88 1HA 0.713287 0.955056
89 01K 0.708333 0.977012
90 COT 0.703448 0.977012
91 CCQ 0.695652 0.934066
92 CA3 0.693878 0.977012
93 CA5 0.671053 0.934066
94 UCA 0.666667 0.955056
95 93P 0.666667 0.965909
96 CO7 0.664234 0.977012
97 93M 0.64557 0.965909
98 OXT 0.634146 0.913979
99 5TW 0.607143 0.913979
100 4BN 0.607143 0.913979
101 PAP 0.603604 0.811765
102 JBT 0.598837 0.894737
103 BSJ 0.592814 0.944444
104 HMG 0.581081 0.943182
105 COA MYR 0.573333 0.922222
106 PLM COA 0.573333 0.922222
107 COA PLM 0.573333 0.922222
108 A3P 0.54955 0.8
109 PPS 0.547009 0.752688
110 0WD 0.521739 0.788889
111 RFC 0.490683 0.955056
112 SFC 0.490683 0.955056
113 191 0.490196 0.865979
114 3AM 0.482143 0.788235
115 PTJ 0.48062 0.872093
116 ACE SER ASP ALY THR NH2 COA 0.478261 0.932584
117 4PS 0.477477 0.682353
118 A22 0.468254 0.813953
119 A2D 0.465517 0.802326
120 PUA 0.462585 0.820225
121 PAJ 0.460938 0.883721
122 AGS 0.459016 0.806818
123 SAP 0.459016 0.806818
124 ATR 0.459016 0.8
125 3OD 0.458015 0.825581
126 ADP 0.453782 0.823529
127 A2R 0.448819 0.813953
128 BA3 0.445378 0.802326
129 NA7 0.442748 0.858824
130 OAD 0.442748 0.825581
131 ATP 0.442623 0.823529
132 AP5 0.441667 0.802326
133 B4P 0.441667 0.802326
134 APR 0.439024 0.802326
135 5FA 0.439024 0.823529
136 2A5 0.439024 0.847059
137 AQP 0.439024 0.823529
138 AR6 0.439024 0.802326
139 AN2 0.438017 0.813953
140 48N 0.435714 0.808989
141 M33 0.434426 0.813953
142 SRP 0.429688 0.837209
143 ANP 0.428571 0.804598
144 ADQ 0.427481 0.804598
145 YLB 0.426573 0.908046
146 YLP 0.425532 0.886364
147 5AL 0.425197 0.813953
148 7D3 0.425 0.793103
149 AD9 0.424 0.804598
150 APU 0.423611 0.786517
151 7D4 0.422764 0.793103
152 CA0 0.422764 0.804598
153 25L 0.422222 0.813953
154 ATF 0.421875 0.795455
155 NJP 0.421769 0.806818
156 A2P 0.421488 0.788235
157 A A A 0.421053 0.813953
158 8QN 0.419847 0.813953
159 PNS 0.419643 0.682353
160 ACP 0.419355 0.825581
161 NDP 0.417808 0.788889
162 ACQ 0.417323 0.825581
163 A1R 0.416667 0.882353
164 ATP A A A 0.416058 0.770115
165 A 0.415254 0.8
166 AMP 0.415254 0.8
167 FYA 0.414815 0.813953
168 1ZZ 0.414815 0.842697
169 TXA 0.414815 0.816092
170 NB8 0.414815 0.808989
171 AHX 0.413534 0.829545
172 DLL 0.413534 0.793103
173 00A 0.413534 0.758242
174 PAX 0.412903 0.793478
175 OMR 0.409722 0.853933
176 25A 0.409091 0.802326
177 OOB 0.409091 0.793103
178 NPW 0.408163 0.822222
179 WAQ 0.407407 0.860465
180 A A 0.407407 0.781609
181 TAT 0.40625 0.816092
182 4AD 0.406015 0.827586
183 AMO 0.406015 0.837209
184 YAP 0.405797 0.806818
185 FA5 0.405797 0.816092
186 TXP 0.405405 0.829545
187 ABM 0.404959 0.781609
188 PRX 0.404762 0.825581
189 ME8 0.404412 0.842697
190 BIS 0.404412 0.818182
191 AFH 0.404255 0.78022
192 J7V 0.403846 0.778947
193 NAI 0.402778 0.777778
194 ODP 0.402685 0.78022
195 ADX 0.4 0.752688
196 SRA 0.4 0.784091
197 AU1 0.4 0.804598
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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