Receptor
PDB id Resolution Class Description Source Keywords
2J4D 1.9 Å NON-ENZYME: OTHER CRYPTOCHROME 3 FROM ARABIDOPSIS THALIANA ARABIDOPSIS THALIANA DNA-BINDING PROTEIN CRYPTOCHROME FLAVOPROTEIN FAD MITOCHONDRION PLASTID CHROMOPHORE CHLOROPLAST TRANSIT PEPTIDE BLUE-LIGHT RESPONSE
Ref.: CRYPTOCHROME 3 FROM ARABIDOPSIS THALIANA: STRUCTURAL AND FUNCTIONAL ANALYSIS OF ITS COMPLEX WITH A FOLATE LIGHT ANTENNA J.MOL.BIOL. V. 366 954 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAD A:1498;
B:1501;
Valid;
Valid;
none;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
MHF A:1499;
B:1502;
Valid;
Valid;
none;
none;
submit data
457.44 C20 H23 N7 O6 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2J4D 1.9 Å NON-ENZYME: OTHER CRYPTOCHROME 3 FROM ARABIDOPSIS THALIANA ARABIDOPSIS THALIANA DNA-BINDING PROTEIN CRYPTOCHROME FLAVOPROTEIN FAD MITOCHONDRION PLASTID CHROMOPHORE CHLOROPLAST TRANSIT PEPTIDE BLUE-LIGHT RESPONSE
Ref.: CRYPTOCHROME 3 FROM ARABIDOPSIS THALIANA: STRUCTURAL AND FUNCTIONAL ANALYSIS OF ITS COMPLEX WITH A FOLATE LIGHT ANTENNA J.MOL.BIOL. V. 366 954 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 2IJG - MHF C20 H23 N7 O6 c1cc(ccc1C....
2 2J4D - MHF C20 H23 N7 O6 c1cc(ccc1C....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 2IJG - MHF C20 H23 N7 O6 c1cc(ccc1C....
2 2J4D - MHF C20 H23 N7 O6 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 922 families.
1 2IJG - MHF C20 H23 N7 O6 c1cc(ccc1C....
2 2J4D - MHF C20 H23 N7 O6 c1cc(ccc1C....
3 1NP7 - 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: MHF; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 MHF 1 1
2 MEF 0.676471 1
3 TMF 0.588785 0.96
4 FON 0.535714 0.881579
5 TLL 0.521368 0.85
6 21V 0.482143 0.818182
7 DDF 0.482143 0.818182
8 DHF 0.455357 0.84
9 THF 0.420168 0.883117
10 C2F 0.420168 0.848101
11 L34 0.416667 0.777778
12 FFO 0.416667 0.881579
13 LYA 0.415929 0.708861
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2J4D; Ligand: FAD; Similar sites found: 53
This union binding pocket(no: 1) in the query (biounit: 2j4d.bio2) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.02304 0.40237 None
2 1GQ2 OXL 0.01505 0.42513 1.33333
3 2BP1 FLC 0.02031 0.42084 1.38889
4 2X8S AHR AHR AHR 0.03434 0.40508 1.48936
5 3X01 AMP 0.02368 0.41511 1.52672
6 3CV2 OXL 0.01597 0.42789 1.90476
7 3HP9 CF1 0.04445 0.40015 2.28216
8 1KAE HSO 0.03459 0.40097 2.30415
9 1XF1 CIT 0.03174 0.40263 2.47619
10 1EXF GLY 0.006622 0.40095 2.47934
11 4X5S AZM 0.03918 0.40019 2.58621
12 4GLW 0XT 0.03467 0.40092 2.62295
13 4CM4 4NR 0.0359 0.40421 2.77778
14 1E4I NFG 0.001238 0.4939 3.13199
15 3FAL REA 0.02918 0.40104 3.30579
16 1SQL GUN 0.0308 0.40752 3.42466
17 3Q3H UDP 0.02407 0.41332 3.42857
18 4M51 BEZ 0.002043 0.45721 3.51288
19 3QTP 2PG 0.03043 0.40388 3.85488
20 4RW3 TDA 0.0328 0.41136 3.97351
21 1F6D UDP 0.02679 0.40293 3.98936
22 2D2F ADP 0.02531 0.41658 4
23 4LH7 NMN 0.009534 0.43558 4.02477
24 3SHZ 5CO 0.007701 0.43023 4.03458
25 2YIP YIO 0.02343 0.4156 5.07246
26 5EW0 3C7 0.0381 0.40266 5.55556
27 1KKR 2AS 0.001618 0.4779 5.81114
28 1SVI GDP 0.02325 0.40995 6.66667
29 5N53 8NB 0.03438 0.40515 6.66667
30 1XVB BHL BHL 0.02339 0.41545 7.05882
31 1WOG 16D 0.02054 0.42562 7.54098
32 2O1O RIS 0.03423 0.40678 7.6087
33 1DQN IMU 0.02585 0.40756 8.26087
34 1HGX 5GP 0.02725 0.40637 9.28962
35 2V5E SCR 0.03011 0.41386 9.90099
36 1PZM 5GP 0.03242 0.40244 9.95261
37 2XKO AKG 0.04157 0.40165 10.1124
38 1J78 VDY 0.03357 0.40165 10.6987
39 4OKD GLC GLC GLC 0.03952 0.40457 11.4286
40 4DJA DLZ 0.000000001414 0.49348 11.583
41 4DJA FAD 0.000000001414 0.49348 11.583
42 3UMV FAD 0.0000000001013 0.70019 12
43 2WCV FUC 0.02697 0.4066 12.8571
44 4CDN FAD 0.00000000003745 0.70905 30.083
45 4CDN FO1 0.0000000004203 0.51696 30.083
46 1U3D FAD 0.00000000000009248 0.80951 38.1139
47 4I6G FAD 0.00000000001044 0.74768 40.0391
48 4U63 FAD 0.000000000000001443 0.87914 41.9679
49 2J07 FAD 0.000000000001165 0.81767 43.8095
50 2J07 HDF 0.000002236 0.59837 43.8095
51 1DNP FAD 0.00000000000002809 0.83969 45.0106
52 1QNF FAD 0.00000000000002132 0.83408 46.281
53 1QNF HDF 0.0000000000004693 0.57983 46.281
Pocket No.: 2; Query (leader) PDB : 2J4D; Ligand: MHF; Similar sites found: 18
This union binding pocket(no: 2) in the query (biounit: 2j4d.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VBF TPP 0.01251 0.43167 1.14286
2 1QPB PYM 0.02193 0.41655 1.52381
3 1QPB TPP 0.02193 0.41655 1.52381
4 1QM5 GLC GLC GLC PO4 SGC GLC 0.0395 0.40905 2.09524
5 1H9A NAP 0.03697 0.41278 2.8866
6 1H6C NDP 0.04189 0.41128 3.00231
7 4HEQ FMN 0.02272 0.40412 3.42466
8 5EXE 5SR 0.03895 0.40601 3.79747
9 1J99 AND 0.0266 0.41887 4.09556
10 3O26 NDP 0.02704 0.41392 4.50161
11 1Z6Z NAP 0.04125 0.40397 5.31915
12 5KY9 GDP 0.01974 0.40295 5.6338
13 2VHW NAI 0.04528 0.40981 6.36605
14 2ZE7 DST 0.03438 0.40457 7.50988
15 4BG4 ARG 0.01195 0.40436 8.14607
16 5KY4 GDP 0.01508 0.40473 12.5
17 3F6R FMN 0.02327 0.40066 14.8649
18 1DNP MHF 0.001557 0.45114 45.0106
Pocket No.: 3; Query (leader) PDB : 2J4D; Ligand: MHF; Similar sites found: 3
This union binding pocket(no: 3) in the query (biounit: 2j4d.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1VEM GLC GLC 0.03016 0.41053 1.35659
2 4RF7 ARG 0.01793 0.40196 1.52381
3 2ZXG S23 0.03313 0.40333 3.42857
Pocket No.: 4; Query (leader) PDB : 2J4D; Ligand: FAD; Similar sites found: 9
This union binding pocket(no: 4) in the query (biounit: 2j4d.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5TME UDP 0.01475 0.41603 1.71306
2 2Q1A 2KT 0.03241 0.40216 2.04778
3 2BCG GER 0.03543 0.40043 2.86976
4 3HW5 AMP 0.0359 0.40584 4.21456
5 3BP1 GUN 0.02197 0.4063 7.24138
6 4WGF HX2 0.009978 0.41827 7.80488
7 5U9J GER 0.003105 0.45501 13.6095
8 4MTI 2DX 0.04102 0.40286 21.7391
9 1SQK LAR 0.02818 0.40181 32
Feedback