Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAD A:500;
B:500;
C:500;
D:500;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
GOL A:700;
A:701;
B:700;
B:701;
C:700;
C:701;
D:700;
D:701;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
N6C A:600;
B:600;
C:600;
D:600;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Ki = 130 mM
131.173 C6 H13 N O2 CCCCC...
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; 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: N6C; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 N6C 1 1
2 N8C 0.84 0.96875
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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