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Receptor
PDB id Resolution Class Description Source Keywords
3MPI 2.05 Å EC: 1.3.99.7 STRUCTURE OF THE GLUTARYL-COENZYME A DEHYDROGENASE GLUTARYL- COMPLEX DESULFOCOCCUS MULTIVORANS ALPHA-BETA FOLD DEHYDROGENASE OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR PROMOTING AND PREVENTING DECARBOXYLATION IN GLUTARYL-COENZYME A DEHYDROGENAS BIOCHEMISTRY V. 49 5350 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAD A:400;
B:400;
C:400;
D:400;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
GRA A:402;
B:402;
C:402;
D:402;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
881.633 C26 H42 N7 O19 P3 S CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3MPI 2.05 Å EC: 1.3.99.7 STRUCTURE OF THE GLUTARYL-COENZYME A DEHYDROGENASE GLUTARYL- COMPLEX DESULFOCOCCUS MULTIVORANS ALPHA-BETA FOLD DEHYDROGENASE OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR PROMOTING AND PREVENTING DECARBOXYLATION IN GLUTARYL-COENZYME A DEHYDROGENAS BIOCHEMISTRY V. 49 5350 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3MPJ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 3MPI - GRA C26 H42 N7 O19 P3 S CC(C)(CO[P....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3MPJ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 3MPI - GRA C26 H42 N7 O19 P3 S CC(C)(CO[P....
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1UDY - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 3MDE - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 3MDD - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 4L1F - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 2R0N - TGC C25 H40 N7 O19 P3 S2 CC(C)(CO[P....
6 1SIQ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
7 5AHS - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
8 5AF7 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
9 1EGD - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
10 3PFD - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
11 3GQT - UFO C11 H17 N3 CN1CCN(c2c....
12 3GNC - QQQ C10 H12 N2 O3 S CC(C)n1c2c....
13 1JQI - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
14 1BUC - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
15 6AF6 - PRO GLY n/a n/a
16 5ZW2 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
17 5ZW7 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
18 5ZW8 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
19 1UKW - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
20 3MPJ - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
21 3MPI - GRA C26 H42 N7 O19 P3 S CC(C)(CO[P....
22 1RX0 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FAD; Similar ligands found: 128
No: Ligand ECFP6 Tc MDL keys Tc
1 FAD 1 1
2 FAS 1 1
3 FAY 0.859259 0.9875
4 RFL 0.852941 0.963855
5 6FA 0.794118 0.987654
6 FAE 0.751773 0.987654
7 SFD 0.651007 0.860215
8 FDA 0.641892 0.906977
9 FNK 0.602564 0.876405
10 62F 0.572327 0.939024
11 F2N 0.566265 0.886364
12 FMN 0.543307 0.876543
13 FA9 0.526316 0.939759
14 6YU 0.516304 0.860215
15 P6G FDA 0.511628 0.908046
16 FAD NBT 0.508876 0.83871
17 A2D 0.504065 0.875
18 P5F 0.491329 0.941176
19 FAD CNX 0.488506 0.8125
20 AR6 0.488372 0.851852
21 APR 0.488372 0.851852
22 AGS 0.484615 0.811765
23 SAP 0.484615 0.811765
24 M33 0.484375 0.864198
25 BA3 0.484127 0.875
26 HEJ 0.48062 0.851852
27 ATP 0.48062 0.851852
28 ADP 0.480315 0.851852
29 B4P 0.480315 0.875
30 AP5 0.480315 0.875
31 ANP 0.477273 0.831325
32 AQP 0.476923 0.851852
33 5FA 0.476923 0.851852
34 48N 0.469388 0.902439
35 OAD 0.467626 0.876543
36 9X8 0.467626 0.833333
37 FAD NBA 0.467033 0.793814
38 GTA 0.465753 0.892857
39 AN2 0.465116 0.841463
40 AT4 0.465116 0.821429
41 AD9 0.462121 0.831325
42 3OD 0.460993 0.876543
43 RBF 0.460938 0.790123
44 FB0 0.460606 0.835165
45 139 0.460526 0.858824
46 AP0 0.46 0.835294
47 A22 0.459854 0.864198
48 ACP 0.458015 0.853659
49 8QN 0.456522 0.864198
50 PRX 0.454545 0.831325
51 A3R 0.453237 0.86747
52 A1R 0.453237 0.86747
53 G3A 0.452055 0.902439
54 T5A 0.45098 0.872093
55 G5P 0.44898 0.902439
56 ATF 0.448529 0.821429
57 50T 0.44697 0.819277
58 6YZ 0.445255 0.853659
59 ACQ 0.444444 0.853659
60 CNV FAD 0.443182 0.917647
61 ADQ 0.442857 0.853659
62 PAJ 0.442857 0.847059
63 5AL 0.441176 0.864198
64 ADX 0.439394 0.775281
65 CA0 0.439394 0.853659
66 A4P 0.437909 0.831461
67 25L 0.4375 0.864198
68 P33 FDA 0.436464 0.817204
69 5SV 0.435714 0.793103
70 OMR 0.434211 0.818182
71 TXE 0.434211 0.890244
72 ABM 0.434109 0.829268
73 A 0.433071 0.82716
74 AMP 0.433071 0.82716
75 4AD 0.432624 0.855422
76 ADJ 0.432258 0.818182
77 B5M 0.431507 0.878049
78 B5Y 0.431507 0.878049
79 BIS 0.430556 0.802326
80 SRA 0.429688 0.788235
81 AFH 0.42953 0.825581
82 NXX 0.427632 0.865854
83 DND 0.427632 0.865854
84 UP5 0.427632 0.878049
85 6V0 0.427632 0.857143
86 TXD 0.427632 0.890244
87 DQV 0.426667 0.8875
88 SRP 0.42446 0.843373
89 PR8 0.423611 0.837209
90 T99 0.423358 0.821429
91 TAT 0.423358 0.821429
92 AMO 0.422535 0.865854
93 TXA 0.42069 0.865854
94 FYA 0.42069 0.864198
95 PTJ 0.42069 0.835294
96 CNA 0.420382 0.865854
97 00A 0.41958 0.823529
98 AHX 0.41958 0.835294
99 MAP 0.41844 0.811765
100 NAI 0.418301 0.845238
101 AU1 0.41791 0.831325
102 A12 0.416667 0.843373
103 AP2 0.416667 0.843373
104 25A 0.415493 0.851852
105 9ZA 0.415493 0.845238
106 9ZD 0.415493 0.845238
107 COD 0.415094 0.842697
108 4TC 0.412903 0.879518
109 APC 0.411765 0.843373
110 ME8 0.410959 0.806818
111 1ZZ 0.410959 0.806818
112 NB8 0.410959 0.835294
113 4UW 0.409091 0.825581
114 NAX 0.409091 0.837209
115 F2R 0.408805 0.850575
116 RBY 0.408759 0.843373
117 ADV 0.408759 0.843373
118 P1H 0.405882 0.818182
119 OOB 0.405594 0.864198
120 LAD 0.40411 0.825581
121 A A 0.40411 0.829268
122 UPA 0.403846 0.86747
123 4UU 0.401316 0.833333
124 GA7 0.401316 0.865854
125 A3D 0.401235 0.876543
126 80F 0.401235 0.808989
127 XAH 0.4 0.806818
128 DLL 0.4 0.864198
Ligand no: 2; Ligand: GRA; Similar ligands found: 132
No: Ligand ECFP6 Tc MDL keys Tc
1 GRA 1 1
2 SCA 0.899225 1
3 HXC 0.878788 0.955556
4 MLC 0.869231 1
5 BCO 0.869231 0.977273
6 1HE 0.869231 0.955556
7 CO8 0.865672 0.955556
8 5F9 0.859259 0.955556
9 MFK 0.859259 0.955556
10 MYA 0.859259 0.955556
11 ST9 0.859259 0.955556
12 UCC 0.859259 0.955556
13 DCC 0.859259 0.955556
14 1VU 0.853846 0.966292
15 HGG 0.849624 1
16 TGC 0.844444 0.988636
17 3HC 0.840909 0.988506
18 IVC 0.840909 0.988506
19 ACO 0.837209 0.966292
20 CAA 0.834586 0.988506
21 OXK 0.832061 1
22 CMX 0.829457 0.977012
23 YNC 0.828571 0.966292
24 3KK 0.824427 0.977273
25 3CP 0.822222 0.977273
26 CAO 0.821705 0.944444
27 COS 0.821705 0.955056
28 FAQ 0.816176 0.977273
29 CO6 0.81203 0.977273
30 CMC 0.81203 0.977273
31 MCA 0.807407 0.988636
32 CS8 0.807143 0.945055
33 2MC 0.80597 0.934783
34 SCO 0.801527 0.977012
35 FYN 0.796992 0.977012
36 COO 0.794118 0.977273
37 SCD 0.792593 0.977012
38 COK 0.791045 0.955056
39 SOP 0.791045 0.955056
40 HDC 0.788732 0.955556
41 MC4 0.788321 0.924731
42 1CZ 0.785714 0.988636
43 COA 0.784615 0.977012
44 0T1 0.784615 0.954545
45 DCA 0.782946 0.932584
46 COW 0.782609 0.966292
47 2KQ 0.782609 0.977528
48 BYC 0.782609 0.977273
49 1GZ 0.782609 0.966292
50 IRC 0.782609 0.988506
51 FCX 0.781955 0.944444
52 30N 0.780303 0.894737
53 AMX 0.780303 0.965517
54 BCA 0.776978 0.966292
55 2CP 0.775362 0.966292
56 A1S 0.773723 0.955056
57 COF 0.769784 0.934066
58 ETB 0.769231 0.9
59 FAM 0.768657 0.933333
60 MCD 0.764706 0.955056
61 HAX 0.762963 0.933333
62 CIC 0.760563 0.977273
63 2NE 0.760563 0.955556
64 CAJ 0.753623 0.955056
65 CA6 0.751825 0.867347
66 4CA 0.751773 0.944444
67 MRR 0.746575 0.955556
68 MRS 0.746575 0.955556
69 NMX 0.746377 0.884211
70 1CV 0.744828 1
71 WCA 0.744828 0.955556
72 4KX 0.739726 0.945055
73 0ET 0.737931 0.934066
74 8Z2 0.736486 0.945055
75 0FQ 0.731034 0.955056
76 4CO 0.731034 0.944444
77 DAK 0.72973 0.945055
78 NHW 0.727891 0.934066
79 UOQ 0.727891 0.934066
80 NHM 0.727891 0.934066
81 01A 0.726027 0.913979
82 CCQ 0.724138 0.934783
83 CA8 0.72028 0.886598
84 YE1 0.71831 0.94382
85 NHQ 0.715232 0.965909
86 UCA 0.71519 0.955556
87 S0N 0.712329 0.955056
88 HFQ 0.711409 0.934066
89 1HA 0.705882 0.955556
90 01K 0.701299 0.955056
91 F8G 0.696774 0.935484
92 COT 0.685897 0.955056
93 7L1 0.685714 0.966292
94 CA3 0.677215 0.955056
95 CA5 0.666667 0.913979
96 93P 0.662577 0.966292
97 CO7 0.659864 0.977273
98 COA PLM 0.657895 0.923077
99 PLM COA 0.657895 0.923077
100 93M 0.652695 0.966292
101 COD 0.637681 0.965517
102 HMG 0.612903 0.965909
103 5TW 0.606742 0.914894
104 4BN 0.606742 0.914894
105 OXT 0.595506 0.914894
106 JBT 0.590164 0.915789
107 BSJ 0.566667 0.945055
108 191 0.544304 0.867347
109 ASP ASP ASP ILE CMC NH2 0.54023 0.933333
110 PAP 0.527559 0.793103
111 SFC 0.505882 0.955556
112 RFC 0.505882 0.955556
113 PPS 0.492424 0.736842
114 ACE SER ASP ALY THR NH2 COA 0.489474 0.933333
115 A3P 0.480315 0.781609
116 0WD 0.467532 0.771739
117 PTJ 0.4375 0.873563
118 3AM 0.421875 0.770115
119 WAQ 0.42069 0.862069
120 PAJ 0.41958 0.885057
121 PUA 0.417178 0.802198
122 A22 0.415493 0.795455
123 A2D 0.409091 0.784091
124 3OD 0.408163 0.827586
125 ATR 0.405797 0.781609
126 AGS 0.405797 0.808989
127 SAP 0.405797 0.808989
128 NA7 0.40411 0.83908
129 YLB 0.401274 0.909091
130 ADP 0.4 0.804598
131 YLP 0.4 0.88764
132 48N 0.4 0.811111
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3MPI; Ligand: GRA; Similar sites found with APoc: 59
This union binding pocket(no: 1) in the query (biounit: 3mpi.bio2) has 88 residues
No: Leader PDB Ligand Sequence Similarity
1 5NNT DPV None
2 6DIO CIT 1.25945
3 3O01 DXC 1.62338
4 5UN9 NHT 1.76322
5 5AZC PGT 2.66667
6 3KO0 TFP 2.9703
7 3HYW DCQ 3.02267
8 5XQL C2E 3.09278
9 5LX9 OLB 3.16901
10 2GWH PCI 3.3557
11 1TO9 HMH 3.46154
12 1H16 PYR 3.52645
13 6MFL OPV 3.57143
14 5WBF LAC 3.7037
15 1SWG BTN 3.90625
16 2BCG GER 4.03023
17 4JNJ BTN 4.34783
18 3B6O TMP 4.45344
19 3EW2 BTN 5.18518
20 3TDC 0EU 5.28967
21 6CB2 OLC 5.54156
22 5XJ7 87O 5.97015
23 3BRE C2E 6.14525
24 4WGF HX2 6.34146
25 4Z28 BTN 6.71642
26 5OCA 9QZ 6.72269
27 5CX6 CDP 6.80101
28 1DQE BOM 8.0292
29 1GPM AMP 8.06045
30 2HHP FLC 8.56423
31 2ZUX RAM 9.57179
32 1PU7 39A 9.63303
33 4NTO 1PW 9.66184
34 3KP6 SAL 9.93377
35 5MR6 FAD 10.8312
36 4RJD TFP 12.1212
37 4OGQ 7PH 16.2011
38 2XN5 FUN 17.1429
39 5ZCO CHD 17.6471
40 5Z84 CHD 17.6471
41 2YYJ 4HP 18.6398
42 2YYJ FAD 18.6398
43 5Y9D FAD 20.403
44 5YS9 FAD 21.1587
45 2DDH HXD 22.67
46 2DDH FAD 22.67
47 4XVX P6G FDA 26.4781
48 4XVX P33 FDA 26.4781
49 3MKH FAD 29.471
50 2Y69 CHD 31.25
51 3DJL FAD 32.7456
52 4Y9J UCC 33.7531
53 4Y9J FAD 33.7531
54 4KCF FMN 38.2872
55 2C0U FAD NBT 40.0504
56 3D9F N6C 40.3023
57 3D9F FAD 40.3023
58 4X28 FDA 42.3592
59 1R2J FAD 48.0874
Pocket No.: 2; Query (leader) PDB : 3MPI; Ligand: GRA; 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: 3mpi.bio2) has 88 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3MPI; Ligand: FAD; Similar sites found with APoc: 29
This union binding pocket(no: 3) in the query (biounit: 3mpi.bio2) has 71 residues
No: Leader PDB Ligand Sequence Similarity
1 4M3P HCS 2.01511
2 3KO0 TFP 2.9703
3 5K8P 6R8 3.29412
4 6MFL OPV 3.57143
5 3IX1 NFM 4.30464
6 2OG2 MLI 7.24234
7 3TUR DGL 8.01394
8 1GPM AMP 8.06045
9 2ZUX RAM 9.57179
10 1PU7 39A 9.63303
11 5MR6 FAD 10.8312
12 2YYJ 4HP 18.6398
13 2YYJ FAD 18.6398
14 5Y9D FAD 20.403
15 5YS9 FAD 21.1587
16 2DDH FAD 22.67
17 2DDH HXD 22.67
18 4XVX P6G FDA 26.4781
19 4XVX P33 FDA 26.4781
20 3MKH FAD 29.471
21 3DJL FAD 32.7456
22 4Y9J UCC 33.7531
23 4Y9J FAD 33.7531
24 4KCF FMN 38.2872
25 2C0U FAD NBT 40.0504
26 3D9F FAD 40.3023
27 3D9F N6C 40.3023
28 4X28 FDA 42.3592
29 1R2J FAD 48.0874
Pocket No.: 4; Query (leader) PDB : 3MPI; Ligand: FAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3mpi.bio2) has 71 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3MPI; Ligand: GRA; Similar sites found with APoc: 26
This union binding pocket(no: 5) in the query (biounit: 3mpi.bio2) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 2Z9I GLY ALA THR VAL 1.85185
2 5VRH OLB 2.267
3 4QEK GLC 2.51889
4 6CGN DA 2.51889
5 5V3Y 5V8 2.7972
6 2HJR CIT 3.04878
7 3HSS MLA 3.07167
8 2QCX PF1 3.42205
9 5IM3 DTP 3.52645
10 3NB0 G6P 3.52645
11 5M37 9SZ 4.78261
12 3KVY URA 5.50162
13 4ZZE GLC GLC GLC 5.55556
14 1NF8 BOG 5.79345
15 2RH1 CLR 5.79345
16 2ALG DAO 6.52174
17 2OG2 MLI 7.24234
18 5LWY OLB 7.56302
19 1M2Z BOG 7.7821
20 1HBK MYR 7.86517
21 4W6Z ETF 8.64553
22 2WOR 2AN 11
23 4OGQ SQD 16.2011
24 1GUX ASP LEU TYR CYS TYR GLU GLN LEU ASN 16.8766
25 5W97 CHD 17.6471
26 5M36 9SZ 21.0526
Pocket No.: 6; Query (leader) PDB : 3MPI; Ligand: GRA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3mpi.bio2) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3MPI; Ligand: FAD; Similar sites found with APoc: 7
This union binding pocket(no: 7) in the query (biounit: 3mpi.bio2) has 70 residues
No: Leader PDB Ligand Sequence Similarity
1 1C3X 8IG 3.00752
2 2HYQ MAN MAN 3.27869
3 4AP9 1PS 3.9801
4 5EHS 5OY 5.22388
5 5EHS 2JJ 5.22388
6 6C0B MLI 6.41026
7 4NTO 1PW 9.66184
Pocket No.: 8; Query (leader) PDB : 3MPI; Ligand: FAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 3mpi.bio2) has 70 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 3MPI; Ligand: FAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 3mpi.bio1) has 69 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 3MPI; Ligand: FAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 3mpi.bio1) has 69 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 3MPI; Ligand: GRA; Similar sites found with APoc: 3
This union binding pocket(no: 11) in the query (biounit: 3mpi.bio1) has 87 residues
No: Leader PDB Ligand Sequence Similarity
1 5I8F ML1 3.63636
2 4AP9 1PS 3.9801
3 2XN3 ID8 15
Pocket No.: 12; Query (leader) PDB : 3MPI; Ligand: GRA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 3mpi.bio1) has 87 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 13; Query (leader) PDB : 3MPI; Ligand: FAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 13) in the query (biounit: 3mpi.bio1) has 70 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 14; Query (leader) PDB : 3MPI; Ligand: FAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 14) in the query (biounit: 3mpi.bio1) has 70 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 15; Query (leader) PDB : 3MPI; Ligand: GRA; Similar sites found with APoc: 1
This union binding pocket(no: 15) in the query (biounit: 3mpi.bio1) has 87 residues
No: Leader PDB Ligand Sequence Similarity
1 4UZI IMD 12.8463
Pocket No.: 16; Query (leader) PDB : 3MPI; Ligand: GRA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 16) in the query (biounit: 3mpi.bio1) has 87 residues
No: Leader PDB Ligand Sequence Similarity
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