Receptor
PDB id Resolution Class Description Source Keywords
3GSI 2 Å EC: 1.5.3.10 CRYSTAL STRUCTURE OF D552A DIMETHYLGLYCINE OXIDASE MUTANT OF ARTHROBACTER GLOBIFORMIS IN COMPLEX WITH TETRAHYDROFOLATE ARTHROBACTER GLOBIFORMIS OXIDOREDUCTASE CHANNELLING FAD BINDING FOLINIC ACID FOLATE BINDING AMINE OXIDATION
Ref.: AN INTERNAL REACTION CHAMBER IN DIMETHYLGLYCINE OXIDASE PROVIDES EFFICIENT PROTECTION FROM EXPOSURE TO TOXIC FORMALDEHYDE. J.BIOL.CHEM. V. 284 17826 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAD A:902;
Valid;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
MG A:901;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
THG A:2887;
Valid;
none;
submit data
445.429 C19 H23 N7 O6 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1PJ6 1.65 Å EC: 1.5.3.10 CRYSTAL STRUCTURE OF DIMETHYLGLYCINE OXIDASE OF ARTHROBACTER GLOBIFORMIS IN COMPLEX WITH FOLIC ACID ARTHROBACTER GLOBIFORMIS CHANNELLING FOLATE BINDING FAD BINDING AMINE OXIDATION OXIDOREDUCTASE
Ref.: CHANNELLING AND FORMATION OF 'ACTIVE' FORMALDEHYDE DIMETHYLGLYCINE OXIDASE. EMBO J. V. 22 4038 2003
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3GSI - THG C19 H23 N7 O6 c1cc(ccc1C....
2 1PJ6 - FOL C19 H19 N7 O6 c1cc(ccc1C....
3 1PJ7 - FFO C20 H23 N7 O7 c1cc(ccc1C....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3GSI - THG C19 H23 N7 O6 c1cc(ccc1C....
2 1PJ6 - FOL C19 H19 N7 O6 c1cc(ccc1C....
3 1PJ7 - FFO C20 H23 N7 O7 c1cc(ccc1C....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3GSI - THG C19 H23 N7 O6 c1cc(ccc1C....
2 1PJ6 - FOL C19 H19 N7 O6 c1cc(ccc1C....
3 1PJ7 - FFO C20 H23 N7 O7 c1cc(ccc1C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FAD; Similar ligands found: 119
No: Ligand ECFP6 Tc MDL keys Tc
1 FAS 1 1
2 FAD 1 1
3 FAY 0.859259 0.9875
4 RFL 0.852941 0.963855
5 6FA 0.794118 0.987654
6 DAL FAD PER 0.772414 0.951807
7 FAE 0.751773 0.987654
8 SFD 0.651007 0.860215
9 FDA 0.641892 0.906977
10 FNK 0.602564 0.876405
11 62F 0.572327 0.939024
12 F2N 0.566265 0.886364
13 FMN 0.543307 0.876543
14 FA9 0.526316 0.939759
15 6YU 0.516304 0.860215
16 CNV FAD 0.511905 0.908046
17 P6G FDA 0.511628 0.908046
18 FAD NBT 0.508876 0.83871
19 A2D 0.504065 0.875
20 P5F 0.491329 0.941176
21 FAD CNX 0.488506 0.8125
22 APR 0.488372 0.851852
23 AR6 0.488372 0.851852
24 AGS 0.484615 0.811765
25 SAP 0.484615 0.811765
26 M33 0.484375 0.864198
27 BA3 0.484127 0.875
28 FAD NBA 0.480663 0.802083
29 ATP 0.48062 0.851852
30 B4P 0.480315 0.875
31 ADP 0.480315 0.851852
32 AP5 0.480315 0.875
33 ANP 0.477273 0.831325
34 AQP 0.476923 0.851852
35 5FA 0.476923 0.851852
36 48N 0.469388 0.902439
37 OAD 0.467626 0.876543
38 GTA 0.465753 0.892857
39 AN2 0.465116 0.841463
40 AD9 0.462121 0.831325
41 3OD 0.460993 0.876543
42 RBF 0.460938 0.790123
43 FB0 0.460606 0.835165
44 139 0.460526 0.858824
45 AP0 0.46 0.835294
46 A22 0.459854 0.864198
47 ACP 0.458015 0.853659
48 8QN 0.456522 0.864198
49 PRX 0.454545 0.831325
50 A1R 0.453237 0.86747
51 G3A 0.452055 0.902439
52 T5A 0.45098 0.872093
53 G5P 0.44898 0.902439
54 ATF 0.448529 0.821429
55 50T 0.44697 0.819277
56 ACQ 0.444444 0.853659
57 PAJ 0.442857 0.847059
58 ADQ 0.442857 0.853659
59 5AL 0.441176 0.864198
60 ADX 0.439394 0.775281
61 CA0 0.439394 0.853659
62 A4P 0.437909 0.831461
63 25L 0.4375 0.864198
64 P33 FDA 0.436464 0.817204
65 5SV 0.435714 0.793103
66 TXE 0.434211 0.890244
67 OMR 0.434211 0.818182
68 ABM 0.434109 0.829268
69 A 0.433071 0.82716
70 AMP 0.433071 0.82716
71 4AD 0.432624 0.855422
72 ADJ 0.432258 0.818182
73 BIS 0.430556 0.802326
74 SRA 0.429688 0.788235
75 AFH 0.42953 0.825581
76 TXD 0.427632 0.890244
77 NXX 0.427632 0.865854
78 UP5 0.427632 0.878049
79 DND 0.427632 0.865854
80 6V0 0.427632 0.857143
81 SRP 0.42446 0.843373
82 PR8 0.423611 0.837209
83 TAT 0.423358 0.821429
84 AMO 0.422535 0.865854
85 PTJ 0.42069 0.835294
86 FYA 0.42069 0.864198
87 TXA 0.42069 0.865854
88 CNA 0.420382 0.865854
89 00A 0.41958 0.823529
90 AHX 0.41958 0.835294
91 MAP 0.41844 0.811765
92 NAI 0.418301 0.845238
93 AU1 0.41791 0.831325
94 AP2 0.416667 0.843373
95 A12 0.416667 0.843373
96 25A 0.415493 0.851852
97 AMP MG 0.415385 0.785714
98 COD 0.415094 0.842697
99 ADP BEF 0.414815 0.77907
100 BEF ADP 0.414815 0.77907
101 4TC 0.412903 0.879518
102 APC 0.411765 0.843373
103 NB8 0.410959 0.835294
104 ME8 0.410959 0.806818
105 1ZZ 0.410959 0.806818
106 4UW 0.409091 0.825581
107 NAX 0.409091 0.837209
108 RBY 0.408759 0.843373
109 ADV 0.408759 0.843373
110 ADP MG 0.407407 0.797619
111 P1H 0.405882 0.818182
112 OOB 0.405594 0.864198
113 A A 0.40411 0.829268
114 LAD 0.40411 0.825581
115 UPA 0.403846 0.86747
116 4UU 0.401316 0.833333
117 A3D 0.401235 0.876543
118 DLL 0.4 0.864198
119 XAH 0.4 0.806818
Ligand no: 2; Ligand: THG; Similar ligands found: 26
No: Ligand ECFP6 Tc MDL keys Tc
1 THG 1 1
2 1YJ 1 1
3 1YA 0.66 0.954545
4 C2F 0.623762 0.887324
5 FFO 0.617647 0.926471
6 FON 0.518182 0.926471
7 THF 0.490909 0.873239
8 9L9 0.484848 0.892308
9 TLL 0.478632 0.863014
10 MEF 0.469027 0.84
11 DHF 0.462963 1
12 THH 0.455357 0.733333
13 GHC 0.454545 0.684211
14 3TZ 0.452174 0.774648
15 29C 0.452174 0.838235
16 29D 0.452174 0.838235
17 28Z 0.452174 0.838235
18 83A 0.45045 0.826087
19 GHW 0.449541 0.693333
20 FOL 0.428571 0.863636
21 DZF 0.428571 0.848485
22 LYA 0.422018 0.782609
23 DXZ 0.401786 0.777778
24 DXY 0.401786 0.777778
25 21V 0.4 0.910448
26 DDF 0.4 0.910448
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1PJ6; Ligand: FOL; Similar sites found: 15
This union binding pocket(no: 1) in the query (biounit: 1pj6.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CQE CQE 0.01155 0.40969 2.15827
2 1OFL NGK GCD 0.009743 0.43079 2.4948
3 2VDF OCT 0.001659 0.40271 2.7668
4 2G30 ALA ALA PHE 0.00006101 0.51444 3.10078
5 3G5D 1N1 0.02542 0.40363 4.54545
6 5TH5 MET 0.01612 0.41208 4.56274
7 1OUK 084 0.03941 0.41704 7.9235
8 5HCY 60D 0.006571 0.42593 9.06344
9 2XG5 EC5 0.001406 0.47329 16.763
10 2XG5 EC2 0.001406 0.47329 16.763
11 5L2J 6UL 0.04283 0.40136 19.3878
12 5X1M THG 0.00007442 0.50152 27.0042
13 5X1M DHB 0.00006938 0.50123 27.0042
14 3TFJ THG 0.000001595 0.51499 36.5854
15 4PAB THG 0.000000003012 0.63651 49.8795
Pocket No.: 2; Query (leader) PDB : 1PJ6; Ligand: FOL; Similar sites found: 103
This union binding pocket(no: 2) in the query (biounit: 1pj6.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CCO OGA 0.0362 0.40444 1.49893
2 2YP9 SIA CMO 0.002525 0.43126 1.59046
3 4JWX 1N4 0.02061 0.41575 1.78571
4 2RDT FMN 0.000005975 0.4402 1.80879
5 2RDT 2RD 0.00008797 0.42011 1.80879
6 3I8P 840 0.004268 0.42426 1.92771
7 1TV5 ORO 0.0002046 0.47405 2.0316
8 1TV5 N8E 0.001731 0.43158 2.0316
9 1TV5 A26 0.001759 0.42033 2.0316
10 1ONX ASP 0.00000769 0.48361 2.05128
11 1Z4V DAN 0.000006381 0.40582 2.06767
12 2WLT ASP 0.0001051 0.43974 2.10843
13 3MAG 3MA 0.02522 0.44518 2.28013
14 2ZO9 MLI 0.01089 0.41749 2.55474
15 3UXL CFI 0.000008367 0.42199 2.61097
16 2E1A MSE 0.00978 0.42595 2.66667
17 4LHM AZZ 0.007895 0.44005 2.72727
18 2Z5Y HRM 0.000006547 0.47695 2.72904
19 3EAU PDN 0.000000692 0.48316 2.75229
20 3EAU NDP 0.000000692 0.48316 2.75229
21 2P2V CSF 0.00000716 0.43385 2.77778
22 1ME8 RVP 0.00000902 0.45367 2.7833
23 3TI8 LNV 0.00004405 0.41882 2.78481
24 2NCD ADP 0.03743 0.40795 2.85714
25 4A8T PAO 0.000032 0.4279 2.94985
26 4Q0P 0MK 0.00000196 0.4803 3.07692
27 1PEA ACM 0.02664 0.43058 3.11688
28 1SQ5 PAU 0.02484 0.41202 3.24675
29 2PP3 LGT 0.003524 0.43169 3.26633
30 3BY8 MLT 0.04863 0.41154 3.52113
31 1Y42 TYR 0.0289 0.40898 3.57143
32 1ZK4 NAP 0.0003105 0.41303 3.58566
33 1ZK4 AC0 0.0003105 0.41303 3.58566
34 1JQN DCO 0.00009273 0.42803 3.61446
35 4Q0A 4OA 0.005046 0.41401 3.64238
36 1P4C FMN 0.00009523 0.41922 3.68421
37 1FW1 GSH 0.009688 0.41375 3.7037
38 1F1V DHY 0.01092 0.42382 3.71517
39 2C9O ADP 0.000145 0.42559 3.72807
40 1FNZ A2G 0.0001024 0.46379 3.79747
41 2Q37 3AL 0.01519 0.42661 3.8674
42 1SAY PYR 0.001921 0.40726 3.87812
43 1DXY NAD 0.0001888 0.42497 3.9039
44 1V6A TRE 0.0392 0.40699 3.91566
45 1NVV GNP 0.000002521 0.44943 4.21687
46 2BMK PDD 0.02813 0.4211 4.22535
47 2BJF DXC 0.00004685 0.41264 4.25532
48 2WL9 MBD 0.002727 0.40734 4.2623
49 1GR0 NAD 0.000005174 0.45682 4.35967
50 1K97 ASP 0.00002475 0.44353 4.3956
51 1K97 CIR 0.00002475 0.44353 4.3956
52 1YOA FAD 0.004167 0.40714 4.40252
53 4Q3S X7A 0.001472 0.40866 4.41558
54 4QN6 LNV 0.00001805 0.40544 4.60358
55 3OYZ ACO 0.00006899 0.42096 4.61894
56 3O9P MHI 0.0003376 0.4044 4.62428
57 1Y9Q MED 0.01783 0.42832 4.6875
58 1G8S MET 0.02328 0.42264 4.78261
59 2Z9V PXM 0.003711 0.44988 4.84694
60 4COQ SAN 0.01003 0.44056 4.8583
61 3NKT 1HN 0.001116 0.41402 4.8913
62 1I0Z OXM 0.01756 0.44673 5.40541
63 2C5S AMP 0.01726 0.41496 5.56901
64 2QV7 ADP 0.00226 0.43523 5.63798
65 3D2M COA 0.0001305 0.43279 5.70175
66 3UC5 ATP 0.0001369 0.4094 5.73248
67 1W7J ADP BEF 0.01085 0.40469 5.96026
68 3WSJ MK1 0.0000286 0.40242 6.03448
69 3C2O NTM 0.001093 0.40425 6.12245
70 1SJW NGV 0.00003219 0.42821 6.25
71 2QLX RM4 0.03503 0.41886 6.48148
72 1RZM E4P 0.02215 0.42901 6.50888
73 1RZM PEP 0.02886 0.40901 6.50888
74 1RN8 DUP 0.003699 0.40436 6.57895
75 2BJK NAD 0.000168 0.40312 6.58915
76 1LGT BP3 0.0003281 0.43046 6.73401
77 1YBQ BDH 0.000001408 0.47162 6.92308
78 2QCX PF1 0.02939 0.41298 7.22433
79 3NGU ADP 0.002488 0.43786 7.28477
80 2PN6 GLN 0.0001309 0.41872 7.33333
81 2F2U M77 0.00358 0.4404 9.20398
82 2RHW C0E 0.0000202 0.43294 9.54064
83 3QVL 5HY 0.00004291 0.41609 9.79592
84 4F4S EFO 0.005784 0.44107 10.5263
85 2PR5 FMN 0.004056 0.41761 10.6061
86 1UF5 CDT 0.01864 0.40944 10.8911
87 4F8L GAL 0.02549 0.45289 11.0345
88 1SS4 GSH 0.0002782 0.57416 11.1111
89 1SS4 CIT 0.004468 0.50271 11.1111
90 1WKL ADP 0.000005299 0.4261 11.6788
91 4IEN COA 0.0004262 0.412 12.2699
92 3SHR CMP 0.02195 0.40635 12.3746
93 3RF4 FUN 0.006003 0.44033 12.931
94 1EYE PMM 0.01886 0.40544 13.9286
95 1QD0 RR6 0.016 0.40846 14.0625
96 3KPE TM3 0.02152 0.42432 15.3846
97 1YRX FMN 0.01266 0.40899 15.7025
98 1TUV VK3 0.02795 0.43569 15.7895
99 2V5E SCR 0.01787 0.45372 15.8416
100 1CFV E3G 0.00002773 0.46994 16.8067
101 1T0S BML 0.005717 0.46564 17.4419
102 1N9L FMN 0.002156 0.42798 20.1835
103 1UGX GAL MGC 0.0006983 0.41436 30
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