Receptor
PDB id Resolution Class Description Source Keywords
3D9G 2.15 Å EC: 1.7.3.1 NITROALKANE OXIDASE: WILD TYPE CRYSTALLIZED IN A TRAPPED STA A CYANOADDUCT WITH FAD FUSARIUM OXYSPORUM OXIDOREDUCTASE FLAVOENZYME NITROALKANE ACYL-COA DEHYDROGELONG CELL EDGE FAD INHIBITOR FLAVOPROTEIN
Ref.: CRYSTAL STRUCTURES OF INTERMEDIATES IN THE NITROALK OXIDASE REACTION. BIOCHEMISTRY V. 48 3407 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAD CNX A:500;
B:500;
C:500;
D:500;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
894.729 n/a [P+](...
GOL A:700;
D:701;
Invalid;
Invalid;
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
3D9F 2.2 Å EC: 1.7.3.1 NITROALKANE OXIDASE: ACTIVE SITE MUTANT S276A CRYSTALLIZED W NITROHEXANE FUSARIUM OXYSPORUM OXIDOREDUCTASE FLAVOENZYME NITROALKANE ACYL-COA DEHYDROGELONG CELL EDGE FAD INHIBITOR FLAVOPROTEIN
Ref.: CRYSTAL STRUCTURES OF INTERMEDIATES IN THE NITROALK OXIDASE REACTION. BIOCHEMISTRY V. 48 3407 2009
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2ZAF - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 3D9F Ki = 130 mM N6C C6 H13 N O2 CCCCCC[N+]....
3 3D9E - N8C C8 H17 N O2 CCCCCCCC[N....
4 2REH - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 2C12 Ki ~ 200 mM SPM C10 H26 N4 C(CCNCCCN)....
6 3D9G - FAD CNX n/a n/a
7 3D9D - N6C C6 H13 N O2 CCCCCC[N+]....
8 3FCJ - NIE C2 H5 N O2 CC[N+](=O)....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2ZAF - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 3D9F Ki = 130 mM N6C C6 H13 N O2 CCCCCC[N+]....
3 3D9E - N8C C8 H17 N O2 CCCCCCCC[N....
4 2REH - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 2C12 Ki ~ 200 mM SPM C10 H26 N4 C(CCNCCCN)....
6 3D9G - FAD CNX n/a n/a
7 3D9D - N6C C6 H13 N O2 CCCCCC[N+]....
8 3FCJ - NIE C2 H5 N O2 CC[N+](=O)....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2ZAF - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 3D9F Ki = 130 mM N6C C6 H13 N O2 CCCCCC[N+]....
3 3D9E - N8C C8 H17 N O2 CCCCCCCC[N....
4 2REH - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 2C12 Ki ~ 200 mM SPM C10 H26 N4 C(CCNCCCN)....
6 3D9G - FAD CNX n/a n/a
7 3D9D - N6C C6 H13 N O2 CCCCCC[N+]....
8 3FCJ - NIE C2 H5 N O2 CC[N+](=O)....
9 3MKH - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FAD CNX; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 FAD CNX 1 1
2 FAD NBT 0.786667 0.85
3 FAD NBA 0.745342 0.947917
4 CNV FAD 0.733766 0.894737
5 FNK 0.613497 0.885417
6 P6G FDA 0.578035 0.85567
7 F2N 0.568965 0.894737
8 DAL FAD PER 0.560694 0.814433
9 FDA 0.551515 0.873684
10 6YU 0.528796 0.888889
11 P33 FDA 0.508287 0.848485
12 SFD 0.49711 0.715596
13 FAD 0.488506 0.8125
14 FAS 0.488506 0.8125
15 6FA 0.468571 0.804124
16 62F 0.461111 0.783505
17 ADP PO3 0.460993 0.723404
18 ATP MG 0.457746 0.701031
19 RFL 0.456044 0.787879
20 FAY 0.450549 0.802083
21 ALF ADP 0.448276 0.68
22 ADP ALF 0.448276 0.68
23 4TA 0.442424 0.831579
24 ADP MG 0.439716 0.701031
25 MYR AMP 0.437909 0.821053
26 BEF ADP 0.43662 0.686869
27 ADP BEF 0.43662 0.686869
28 ADP VO4 0.435374 0.701031
29 VO4 ADP 0.435374 0.701031
30 ALF ADP 3PG 0.434783 0.693069
31 LA8 ALF 3PG 0.434783 0.693069
32 AF3 ADP 3PG 0.434783 0.693069
33 FA9 0.434555 0.822917
34 Z5A 0.427746 0.806122
35 ADP BMA 0.427632 0.729167
36 NAJ PZO 0.426035 0.752577
37 ANP MG 0.425676 0.68
38 ATP A A A 0.423077 0.734043
39 P5F 0.418848 0.845361
40 AHZ 0.416149 0.747475
41 NAD IBO 0.410714 0.75
42 OMR 0.408537 0.8125
43 5SV 0.407895 0.789474
44 AMP MG 0.407143 0.690722
45 1ZZ 0.403846 0.802083
46 AR6 AR6 0.403727 0.726316
47 DAL AMP 0.401316 0.736842
48 M33 0.4 0.71875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3D9F; Ligand: N6C; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3d9f.bio1) has 50 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3D9F; Ligand: FAD; Similar sites found: 64
This union binding pocket(no: 2) in the query (biounit: 3d9f.bio1) has 51 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.03462 0.43735 None
2 3RY9 1CA 0.02385 0.41293 1.2
3 1W07 FAD 0.00000691 0.50718 1.82648
4 1BW9 PPY 0.03959 0.40787 1.96629
5 1C1X HFA 0.03774 0.41217 1.97183
6 4O1Z MXM 0.0204 0.40768 2.05479
7 4AMV F6R 0.02472 0.41523 2.28311
8 3HYW DCQ 0.02423 0.43026 2.32558
9 5HCV 60R 0.02977 0.40258 2.33463
10 4DK7 0KS 0.02537 0.40868 2.42915
11 3W54 RNB 0.0377 0.40898 2.43161
12 5UC9 MYR 0.02098 0.42566 2.51142
13 5LX9 OLB 0.01426 0.43078 2.60586
14 2Q8H TF4 0.04415 0.42985 2.7027
15 2I80 G1L 0.04573 0.40773 2.77778
16 1NSA BEN 0.02879 0.42202 2.78481
17 3OKI OKI 0.01586 0.41562 3.00429
18 1NRL SRL 0.01411 0.41803 3.16456
19 4KVL PLM 0.006113 0.42898 3.19635
20 1S20 NAD 0.01885 0.41495 3.23529
21 1NF8 BOG 0.001863 0.50974 3.38164
22 1U8V FAD 0.0005922 0.44326 3.65297
23 3KMR EQN 0.01814 0.41575 3.7594
24 5EVY SAL 0.04272 0.42149 3.88128
25 3AB4 THR 0.04688 0.41398 3.93258
26 3UN3 G16 0.01486 0.4141 4.01003
27 4J26 EST 0.008387 0.44655 4.16667
28 3UU7 2OH 0.04189 0.42178 4.78088
29 2WTN FER 0.03459 0.42133 4.78088
30 5F2T PLM 0.008214 0.42916 4.87013
31 1M2Z BOG 0.01291 0.46303 5.05837
32 1M2Z DEX 0.01894 0.41195 5.05837
33 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.02936 0.44527 5.10204
34 4IBF 1D5 0.04832 0.40336 5.42636
35 4MGA 27L 0.003427 0.48373 5.4902
36 4MGD 27N 0.0302 0.41397 5.4902
37 4MG8 27J 0.04014 0.40756 5.4902
38 4E2J MOF 0.0234 0.40232 6
39 3GN8 DEX 0.02755 0.40419 6.0241
40 1K7L 544 0.01807 0.40246 6.16438
41 1TV5 N8E 0.02185 0.43658 6.32054
42 1ELW GLY PRO THR ILE GLU GLU VAL ASP 0.02529 0.42138 9.32203
43 5OCA 9QZ 0.03382 0.43436 10.3175
44 1XVB 3BR 0.02538 0.42492 10.5882
45 1WQ1 AF3 0.02836 0.43463 12.6506
46 4XVX P6G FDA 0.00003278 0.4042 13.6247
47 2CB8 MYA 0.01133 0.45597 14.9425
48 3GQT UFO 0.006593 0.45202 15.5388
49 4X28 FDA 0.00001088 0.41499 19
50 5K53 STE 0.02006 0.41076 20.6107
51 1R2J FAD 0.0003923 0.50539 21.8579
52 1RX0 FAD 0.000002094 0.44358 37.4046
53 3MPI GRA 0.004652 0.40049 40.3023
54 1JQI FAD 0.000000591 0.46421 41.2371
55 5AHS FAD 0.000009164 0.56837 44.389
56 5AHS COA 0.0001014 0.47936 44.389
57 5AHS SIN 0.01041 0.45561 44.389
58 1UDY CS8 0.00000006182 0.50571 44.4444
59 1UDY FAD 0.00001837 0.40769 44.4444
60 1EGD FAD 0.000000179 0.47004 45.7071
61 4L1F FAD 0.00000009205 0.58587 45.953
62 4L1F COS 0.02116 0.40182 45.953
63 3PFD FDA 0.0000002285 0.48222 46.3104
64 1UKW FAD 0.000002786 0.58667 47.2296
Pocket No.: 3; Query (leader) PDB : 3D9F; Ligand: N6C; Similar sites found: 39
This union binding pocket(no: 3) in the query (biounit: 3d9f.bio1) has 51 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3RY9 1CA 0.02385 0.41293 1.2
2 1W07 FAD 0.00000691 0.43297 1.82648
3 4O1Z MXM 0.0204 0.40768 2.05479
4 5HCV 60R 0.02977 0.40258 2.33463
5 4DK7 0KS 0.02537 0.40868 2.42915
6 5UC9 MYR 0.02098 0.42566 2.51142
7 5LX9 OLB 0.01426 0.43078 2.60586
8 2I80 G1L 0.04573 0.40773 2.77778
9 1NSA BEN 0.02879 0.42202 2.78481
10 3OKI OKI 0.01586 0.41562 3.00429
11 4KVL PLM 0.006113 0.42898 3.19635
12 1S20 NAD 0.01885 0.41495 3.23529
13 1U8V FAD 0.0005922 0.44326 3.65297
14 5EVY SAL 0.04272 0.42149 3.88128
15 3AB4 THR 0.04688 0.41398 3.93258
16 2WTN FER 0.03459 0.42133 4.78088
17 5F2T PLM 0.008214 0.42916 4.87013
18 1M2Z BOG 0.01291 0.46303 5.05837
19 1M2Z DEX 0.01894 0.41195 5.05837
20 4MGA 27L 0.003427 0.48373 5.4902
21 4E2J MOF 0.0234 0.40232 6
22 1K7L 544 0.01807 0.40246 6.16438
23 1TV5 N8E 0.003784 0.49207 6.32054
24 5OCA 9QZ 0.03382 0.43436 10.3175
25 4XVX P6G FDA 0.00003278 0.4042 13.6247
26 3GQT UFO 0.006593 0.45202 15.5388
27 4X28 FDA 0.00001088 0.41499 19
28 5K53 STE 0.02006 0.41076 20.6107
29 1R2J FAD 0.0003923 0.50539 21.8579
30 1RX0 FAD 0.000002094 0.44358 37.4046
31 5AHS FAD 0.000009164 0.56837 44.389
32 5AHS COA 0.0001014 0.47936 44.389
33 5AHS SIN 0.01041 0.45561 44.389
34 1UDY CS8 0.00000006182 0.50571 44.4444
35 1UDY FAD 0.00001837 0.40769 44.4444
36 1EGD FAD 0.000000179 0.47004 45.7071
37 4L1F FAD 0.00000006864 0.59559 45.953
38 4L1F COS 0.02116 0.40182 45.953
39 3PFD FDA 0.0000002285 0.48222 46.3104
Pocket No.: 4; Query (leader) PDB : 3D9F; Ligand: FAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3d9f.bio1) has 44 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3D9F; Ligand: FAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3d9f.bio1) has 50 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3D9F; Ligand: N6C; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3d9f.bio1) has 51 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3D9F; Ligand: N6C; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 3d9f.bio1) has 44 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3D9F; Ligand: FAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 3d9f.bio1) has 51 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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