Receptor
PDB id Resolution Class Description Source Keywords
2YG3 2 Å EC: 1.4.3.10 STRUCTURE-BASED REDESIGN OF COFACTOR BINDING IN PUTRESCINE OXIDASE: WILD TYPE ENZYME RHODOCOCCUS ERYTHROPOLIS OXIDOREDUCTASE FLAVIN
Ref.: STRUCTURE-BASED REDESIGN OF COFACTOR BINDING IN PUT OXIDASE. BIOCHEMISTRY V. 50 4209 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAD A:600;
B:600;
 Valid;
Valid;
 none;
none;
 submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
GOL A:1451;
A:1453;
A:1455;
B:1452;
B:1453;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:1452;
A:1454;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2YG3 2 Å EC: 1.4.3.10 STRUCTURE-BASED REDESIGN OF COFACTOR BINDING IN PUTRESCINE OXIDASE: WILD TYPE ENZYME RHODOCOCCUS ERYTHROPOLIS OXIDOREDUCTASE FLAVIN
Ref.: STRUCTURE-BASED REDESIGN OF COFACTOR BINDING IN PUT OXIDASE. BIOCHEMISTRY V. 50 4209 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YG4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 2YG3 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YG4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 2YG3 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YG4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 2YG3 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FAD; Similar ligands found: 136
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 SAP 0.484615 0.811765
23 AGS 0.484615 0.811765
24 M33 0.484375 0.864198
25 BA3 0.484127 0.875
26 ATP 0.48062 0.851852
27 HEJ 0.48062 0.851852
28 AP5 0.480315 0.875
29 B4P 0.480315 0.875
30 ADP 0.480315 0.851852
31 ANP 0.477273 0.831325
32 5FA 0.476923 0.851852
33 AQP 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 AT4 0.465116 0.821429
40 AN2 0.465116 0.841463
41 HQG 0.463235 0.841463
42 AD9 0.462121 0.831325
43 3OD 0.460993 0.876543
44 RBF 0.460938 0.790123
45 FB0 0.460606 0.835165
46 139 0.460526 0.858824
47 AP0 0.46 0.835294
48 A22 0.459854 0.864198
49 ACP 0.458015 0.853659
50 8QN 0.456522 0.864198
51 PRX 0.454545 0.831325
52 A1R 0.453237 0.86747
53 A3R 0.453237 0.86747
54 G3A 0.452055 0.902439
55 T5A 0.45098 0.872093
56 G5P 0.44898 0.902439
57 ATF 0.448529 0.821429
58 50T 0.44697 0.819277
59 OZV 0.446043 0.851852
60 6YZ 0.445255 0.853659
61 ACQ 0.444444 0.853659
62 CNV FAD 0.443182 0.917647
63 PAJ 0.442857 0.847059
64 ADQ 0.442857 0.853659
65 8LE 0.441176 0.855422
66 5AL 0.441176 0.864198
67 CA0 0.439394 0.853659
68 ADX 0.439394 0.775281
69 8LQ 0.438849 0.865854
70 A4P 0.437909 0.831461
71 25L 0.4375 0.864198
72 P33 FDA 0.436464 0.817204
73 KG4 0.43609 0.853659
74 5SV 0.435714 0.793103
75 8LH 0.434783 0.843373
76 OMR 0.434211 0.818182
77 TXE 0.434211 0.890244
78 45A 0.434109 0.829268
79 ABM 0.434109 0.829268
80 AMP 0.433071 0.82716
81 A 0.433071 0.82716
82 4AD 0.432624 0.855422
83 ADJ 0.432258 0.818182
84 B5Y 0.431507 0.878049
85 B5M 0.431507 0.878049
86 BIS 0.430556 0.802326
87 SRA 0.429688 0.788235
88 AFH 0.42953 0.825581
89 NXX 0.427632 0.865854
90 UP5 0.427632 0.878049
91 TXD 0.427632 0.890244
92 6V0 0.427632 0.857143
93 DND 0.427632 0.865854
94 DQV 0.426667 0.8875
95 SRP 0.42446 0.843373
96 PR8 0.423611 0.837209
97 TAT 0.423358 0.821429
98 T99 0.423358 0.821429
99 AMO 0.422535 0.865854
100 FYA 0.42069 0.864198
101 TXA 0.42069 0.865854
102 PTJ 0.42069 0.835294
103 CNA 0.420382 0.865854
104 00A 0.41958 0.823529
105 AHX 0.41958 0.835294
106 MAP 0.41844 0.811765
107 NAI 0.418301 0.845238
108 AU1 0.41791 0.831325
109 AP2 0.416667 0.843373
110 A12 0.416667 0.843373
111 9ZA 0.415493 0.845238
112 9ZD 0.415493 0.845238
113 25A 0.415493 0.851852
114 COD 0.415094 0.842697
115 4TC 0.412903 0.879518
116 APC 0.411765 0.843373
117 ME8 0.410959 0.806818
118 NB8 0.410959 0.835294
119 1ZZ 0.410959 0.806818
120 ADP MG 0.410448 0.82716
121 NAX 0.409091 0.837209
122 4UW 0.409091 0.825581
123 F2R 0.408805 0.850575
124 RBY 0.408759 0.843373
125 ADV 0.408759 0.843373
126 P1H 0.405882 0.818182
127 OOB 0.405594 0.864198
128 A A 0.40411 0.829268
129 LAD 0.40411 0.825581
130 UPA 0.403846 0.86747
131 4UU 0.401316 0.833333
132 GA7 0.401316 0.865854
133 A3D 0.401235 0.876543
134 80F 0.401235 0.808989
135 XAH 0.4 0.806818
136 DLL 0.4 0.864198
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YG3; Ligand: FAD; Similar sites found with APoc: 64
This union binding pocket(no: 1) in the query (biounit: 2yg3.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 3QJ4 FAD 6.43275
2 3QJ4 FAD 6.43275
3 2Z3Y F2N 7.72627
4 3AYI FAD 8.38852
5 3AYI HCI 8.38852
6 3AYI FAD 8.38852
7 3AYI HCI 8.38852
8 4ZCC FAD 9.22619
9 4ZCC NAI 9.22619
10 4ZCC FAD 9.22619
11 4ZCC FAD 9.22619
12 4ZCC NAI 9.22619
13 4ZCC FAD 9.22619
14 4IV9 FAD 9.71302
15 5G3U FDA 26.2411
16 5G3U FDA 26.2411
17 5G3U ITW 26.2411
18 1YY5 FAD 26.7108
19 1YY5 FAD 26.7108
20 1RSG FAD 26.7108
21 1RSG FAD 26.7108
22 5TTJ FAD 38.1898
23 5TTJ FAD 38.1898
24 5MBX FAD 38.1898
25 5MBX SP5 38.1898
26 2JB2 PHE 40.0818
27 2JB2 FAD 40.0818
28 2JB2 PHE 40.0818
29 2JB2 FAD 40.0818
30 2VVL FAD 41.0596
31 2VVL FAD 41.0596
32 2VVL FAD 41.0596
33 2VVL FAD 41.0596
34 2VVL FAD 41.0596
35 2VVL FAD 41.0596
36 2VVL FAD 41.0596
37 2VVL FAD 41.0596
38 2VVM FAD 41.2804
39 2VVM FAD 41.2804
40 2IID PHE 42.3841
41 2IID FAD 42.3841
42 2IID FAD 42.3841
43 2IID PHE 42.3841
44 2IID FAD 42.3841
45 2IID PHE 42.3841
46 2IID FAD 42.3841
47 2IID PHE 42.3841
48 3K7M FAD 43.1555
49 4GUS FAD 43.2671
50 4GUT FAD 43.2671
51 4FWE FAD 43.2671
52 4HSU FAD 43.2671
53 4FWE FAD 43.2671
54 1REO FAD 43.4879
55 5TS5 FAD 43.7086
56 5TS5 FAD 43.7086
57 5TS5 FAD 43.7086
58 5TS5 FAD 43.7086
59 1H82 FAD 43.9294
60 1H82 GZZ 43.9294
61 1H82 GZZ 43.9294
62 1H82 FAD 43.9294
63 1H82 GZZ 43.9294
64 1H82 FAD 43.9294
Pocket No.: 2; Query (leader) PDB : 2YG3; Ligand: FAD; Similar sites found with APoc: 64
This union binding pocket(no: 2) in the query (biounit: 2yg3.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 3QJ4 FAD 6.43275
2 3QJ4 FAD 6.43275
3 2Z3Y F2N 7.72627
4 3AYI FAD 8.38852
5 3AYI HCI 8.38852
6 3AYI FAD 8.38852
7 3AYI HCI 8.38852
8 4ZCC FAD 9.22619
9 4ZCC NAI 9.22619
10 4ZCC FAD 9.22619
11 4ZCC NAI 9.22619
12 4ZCC FAD 9.22619
13 4ZCC FAD 9.22619
14 4IV9 FAD 9.71302
15 5G3U FDA 26.2411
16 5G3U FDA 26.2411
17 5G3U ITW 26.2411
18 1YY5 FAD 26.7108
19 1YY5 FAD 26.7108
20 1RSG FAD 26.7108
21 1RSG FAD 26.7108
22 5TTJ FAD 38.1898
23 5TTJ FAD 38.1898
24 5MBX FAD 38.1898
25 5MBX SP5 38.1898
26 2JB2 PHE 40.0818
27 2JB2 FAD 40.0818
28 2JB2 PHE 40.0818
29 2JB2 FAD 40.0818
30 2VVL FAD 41.0596
31 2VVL FAD 41.0596
32 2VVL FAD 41.0596
33 2VVL FAD 41.0596
34 2VVL FAD 41.0596
35 2VVL FAD 41.0596
36 2VVL FAD 41.0596
37 2VVL FAD 41.0596
38 2VVM FAD 41.2804
39 2VVM FAD 41.2804
40 2IID PHE 42.3841
41 2IID FAD 42.3841
42 2IID FAD 42.3841
43 2IID PHE 42.3841
44 2IID FAD 42.3841
45 2IID PHE 42.3841
46 2IID FAD 42.3841
47 2IID PHE 42.3841
48 3K7M FAD 43.1555
49 4GUS FAD 43.2671
50 4GUT FAD 43.2671
51 4FWE FAD 43.2671
52 4HSU FAD 43.2671
53 4FWE FAD 43.2671
54 1REO FAD 43.4879
55 5TS5 FAD 43.7086
56 5TS5 FAD 43.7086
57 5TS5 FAD 43.7086
58 5TS5 FAD 43.7086
59 1H82 FAD 43.9294
60 1H82 GZZ 43.9294
61 1H82 GZZ 43.9294
62 1H82 FAD 43.9294
63 1H82 GZZ 43.9294
64 1H82 FAD 43.9294
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