Receptor
PDB id Resolution Class Description Source Keywords
5DKK 2.5 Å NON-ENZYME: OTHER STRUCTURE OF THE DARK-STATE MONOMER OF THE BLUE LIGHT PHOTOR AUREOCHROME 1A LOV FROM P. TRICORNUTUM PHAEODACTYLUM TRICORNUTUM LOV DNA BINDING PHOTORECEPTOR SIGNALING PROTEIN FLAVOPROTETRANSCRIPTION
Ref.: BLUE LIGHT-INDUCED LOV DOMAIN DIMERIZATION ENHANCES AFFINITY OF AUREOCHROME 1A FOR ITS TARGET DNA SEQUE ELIFE V. 5 11860 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMN A:401;
B:500;
Valid;
Valid;
none;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
ACT A:402;
A:403;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
EDO A:404;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DKK 2.5 Å NON-ENZYME: OTHER STRUCTURE OF THE DARK-STATE MONOMER OF THE BLUE LIGHT PHOTOR AUREOCHROME 1A LOV FROM P. TRICORNUTUM PHAEODACTYLUM TRICORNUTUM LOV DNA BINDING PHOTORECEPTOR SIGNALING PROTEIN FLAVOPROTETRANSCRIPTION
Ref.: BLUE LIGHT-INDUCED LOV DOMAIN DIMERIZATION ENHANCES AFFINITY OF AUREOCHROME 1A FOR ITS TARGET DNA SEQUE ELIFE V. 5 11860 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5DKK - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5DKK - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 141 families.
1 2PR5 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 1N9L - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 1N9N - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 3T50 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 2Z6C - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
6 4EES - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
7 4EET - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 4NXE - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 4EER - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 4NXG - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
11 4NXF - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 4EEP - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 4EEU - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
14 2V1A - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
15 2V0U - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
16 5DKK - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
17 2Z6D - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FMN; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 RS3 0.571429 0.831169
4 FAS 0.543307 0.876543
5 FAD 0.543307 0.876543
6 FAE 0.539062 0.865854
7 DAL FAD PER 0.5 0.833333
8 LFN 0.475 0.643836
9 C3F 0.473684 0.74359
10 CF4 0.463918 0.734177
11 FAY 0.446043 0.864198
12 FNR 0.444444 0.909091
13 RFL 0.442857 0.845238
14 4LS 0.411215 0.875
15 1VY 0.406593 0.769231
16 DLZ 0.404494 0.782051
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DKK; Ligand: FMN; Similar sites found: 134
This union binding pocket(no: 1) in the query (biounit: 5dkk.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1YRX FMN 0.0002791 0.47005 None
2 4WVW SLT 0.001115 0.46677 None
3 3KP6 SAL 0.008072 0.44574 None
4 2GBB CIT 0.004327 0.43428 None
5 1ECM TSA 0.004921 0.43151 None
6 1SN0 T44 0.00498 0.42205 None
7 2Z77 HE7 0.004656 0.40969 None
8 5T2Z 017 0.01069 0.40615 None
9 1KGI T4A 0.007534 0.40574 None
10 4UCC ZKW 0.01843 0.40512 None
11 2LBD REA 0.00851 0.40496 None
12 4CQE CQE 0.01718 0.40476 None
13 4XV1 904 0.01455 0.40373 None
14 1TT8 PHB 0.01001 0.40331 None
15 4WG0 CHD 0.02311 0.40155 None
16 5TFZ 7BC 0.01872 0.40268 1.37931
17 1HN4 MJI 0.04014 0.40592 1.52672
18 3JRS A8S 0.008375 0.4004 1.92308
19 4DSU BZI 0.002354 0.45881 2.06897
20 4BVA T3 0.002019 0.45012 2.75862
21 1QY1 PRZ 0.001883 0.42862 2.75862
22 4DXJ 0M9 0.01005 0.40736 2.75862
23 5U9J GER 0.001993 0.45654 3.44828
24 3HP9 CF1 0.005933 0.44222 3.44828
25 5HCY 60D 0.00485 0.43544 3.44828
26 1GQG DCD 0.001546 0.43421 3.44828
27 2X4Z X4Z 0.005376 0.42473 3.44828
28 2W5P CL8 0.0139 0.41905 3.44828
29 3LDW ZOL 0.008741 0.41265 3.44828
30 3Q9T FAY 0.02196 0.40078 3.44828
31 2YBP 2HG 0.0112 0.4223 4.13793
32 2Q8E OGA 0.01202 0.42061 4.13793
33 2OS2 OGA 0.01239 0.41992 4.13793
34 2GC0 PAN 0.006289 0.40565 4.13793
35 2B4G FMN 0.01143 0.40215 4.13793
36 3EW2 BTN 0.00105 0.45912 4.44444
37 4Z28 BTN 0.001331 0.45416 4.47761
38 4Z3E GAL NGA GLA BGC GAL 0.0009604 0.47694 4.54545
39 4BG4 ADP 0.0008957 0.44282 4.82759
40 1U6R ADP 0.002164 0.41737 4.82759
41 3OPT AKG 0.01514 0.41546 4.82759
42 5APK 76E 0.008957 0.40828 4.82759
43 2JFZ 003 0.03496 0.4059 4.82759
44 5NTW 98N 0.01148 0.40474 4.82759
45 4WOE ADP 0.00924 0.40337 4.82759
46 1QKQ MAN 0.000179 0.50363 4.92958
47 1SGJ OAA 0.001382 0.43494 4.92958
48 5E89 TD2 0.009921 0.4004 5.03597
49 1A78 TDG 0.006939 0.41951 5.22388
50 4MGA 27L 0.007548 0.43312 5.51724
51 5A5W GUO 0.005997 0.42913 5.51724
52 2CHG ANP 0.002378 0.42421 5.51724
53 5VAD PRO 0.005723 0.41507 5.51724
54 4OCT AKG 0.01205 0.40795 5.51724
55 3ZJX BOG 0.02224 0.40731 5.51724
56 1Y75 NAG 0.01779 0.40378 5.51724
57 3K5I ADP 0.007536 0.40063 5.51724
58 5DQ8 FLF 0.005182 0.4129 5.83333
59 1MDC PLM 0.0005738 0.45302 6.06061
60 4RW3 PLM 0.01933 0.43276 6.2069
61 3G5D 1N1 0.009229 0.43071 6.2069
62 3TKI S25 0.013 0.42199 6.2069
63 4QXB OGA 0.0002986 0.41873 6.2069
64 4TWP AXI 0.01522 0.41293 6.2069
65 4XLI 1N1 0.008548 0.40332 6.2069
66 2XMY CDK 0.0449 0.40232 6.2069
67 1UNQ 4IP 0.02503 0.40103 6.2069
68 1YFS ALA 0.02093 0.4008 6.2069
69 4YZC STU 0.01274 0.40974 6.89655
70 3SHZ 5CO 0.01151 0.40892 6.89655
71 4U63 FAD 0.009681 0.40676 6.89655
72 3WFD AXO 0.01902 0.40583 6.89655
73 2JDR L20 0.03655 0.40233 6.89655
74 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.03655 0.40233 6.89655
75 3E9I XAH 0.01362 0.40139 6.89655
76 1T0S BML 0.01654 0.40086 6.89655
77 3IAL PR8 0.009178 0.40035 6.89655
78 3I27 SID 0.00994 0.42104 7.58621
79 4XBT 3ZQ 0.005947 0.41842 7.58621
80 1W2D ADP 0.01437 0.40424 7.58621
81 1XAP TTB 0.007091 0.40177 7.58621
82 2QZZ NAP 0.02198 0.40076 7.58621
83 4F4P 0SB 0.04283 0.40026 7.58621
84 5L2J 70E 0.02912 0.41348 8.16327
85 1DZK PRZ 0.001104 0.44326 8.27586
86 3LGG CFE 0.008999 0.40602 8.27586
87 3E7O 35F 0.01399 0.40333 8.27586
88 4FFG LBS 0.003801 0.43716 8.96552
89 1HZP DAO 0.006417 0.42875 8.96552
90 1M2Z BOG 0.03073 0.41441 8.96552
91 3T58 FAD 0.008464 0.41203 8.96552
92 4P8K 38C 0.03108 0.40906 8.96552
93 4P8K FAD 0.03018 0.40906 8.96552
94 1JLX GAL A2G MBN 0.02565 0.4012 8.96552
95 5MJA 7O3 0.004962 0.40105 8.96552
96 3A16 PXO 0.01818 0.40024 8.96552
97 2V57 PRL 0.01611 0.41786 9.47368
98 4JNJ BTN 0.002713 0.42998 9.56522
99 2HFN FMN 0.0007655 0.43643 9.65517
100 1VJY 460 0.01018 0.40963 9.65517
101 5IR4 ZPE 0.01716 0.40958 9.65517
102 2IID FAD 0.02835 0.40842 9.65517
103 2IID PHE 0.02835 0.40842 9.65517
104 1EPB REA 0.007307 0.40639 9.65517
105 5A0U CHT 0.01783 0.40807 10.3448
106 1BHX ASP PHE GLU GLU ILE 0.01705 0.40063 10.4762
107 3RGA LSB 0.001299 0.42022 11.0345
108 2HK9 SKM 0.01605 0.41434 11.0345
109 3B6R ADP 0.002598 0.40922 11.0345
110 4O4Z N2O 0.02443 0.40302 11.0345
111 3WYJ H78 0.003017 0.46088 11.7241
112 2GJ5 VD3 0.007529 0.4214 12.4138
113 4MRP GSH 0.006323 0.44765 13.1034
114 2Q0D ATP 0.008803 0.41126 13.1034
115 2B9I ADP 0.007133 0.40324 13.7931
116 3T4L ZEA 0.001157 0.42943 14.4828
117 2AG4 LP3 0.003189 0.45684 15.1724
118 2AG4 OLA 0.002862 0.45684 15.1724
119 1M15 ARG 0.002594 0.43921 15.1724
120 1M15 ADP 0.002594 0.43921 15.1724
121 1WBI BTN 0.005128 0.41726 15.5039
122 1LRI CLR 0.004459 0.41577 16.3265
123 4CJN QNZ 0.03018 0.4006 17.2414
124 1PS9 FAD 0.02594 0.40107 17.931
125 3JQ3 ADP 0.007604 0.41763 18.6207
126 2HFK E4H 0.01264 0.4157 18.6207
127 5DEY 59T 0.01223 0.42326 20
128 1X0P FAD 0.0005015 0.43433 22.3776
129 3EWK FAD 0.00001815 0.5112 30.3448
130 5MBC FMN 0.0005229 0.4396 33.7931
131 2GJ3 FAD 0.02004 0.42157 37.5
132 3P7N FMN 0.0000000000001731 0.85539 44.8276
133 4WUJ FMN 0.000000000001915 0.8106 46.2069
134 4R38 RBF 0.00000000001488 0.77658 47.8571
Pocket No.: 2; Query (leader) PDB : 5DKK; Ligand: FMN; Similar sites found: 35
This union binding pocket(no: 2) in the query (biounit: 5dkk.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1OUK 084 0.02176 0.43023 2.06897
2 3OYW TDG 0.01835 0.40918 2.23881
3 4CPH LH4 0.01306 0.40035 2.3622
4 2D6M LBT 0.005536 0.44545 2.75862
5 3KRR DQX 0.01909 0.41727 2.75862
6 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 0.04535 0.40536 2.75862
7 3QCP FAD 0.001954 0.43108 3.44828
8 3AHQ FAD 0.0009951 0.4214 3.44828
9 3H78 BE2 0.01074 0.40293 3.44828
10 3LLI FAD 0.003396 0.42215 4.13793
11 3GWN FAD 0.003672 0.41061 4.38596
12 1TV5 N8E 0.007102 0.44589 5.51724
13 1U25 IHS 0.02049 0.41731 5.51724
14 4ORM 2V6 0.02594 0.41203 5.51724
15 4ORM ORO 0.02594 0.41203 5.51724
16 4ORM FMN 0.02594 0.41203 5.51724
17 4LY9 S6P 0.02184 0.40596 5.51724
18 4LY9 1YY 0.02355 0.40596 5.51724
19 4YLL 4E3 0.006242 0.40436 5.51724
20 5HCN DAO 0.02361 0.40354 5.51724
21 3IA4 MTX 0.009895 0.40594 6.2069
22 5UIU 8CG 0.01099 0.4025 6.89655
23 4D4U FUC NDG GAL FUC 0.02434 0.40525 7.58621
24 1SZO CAX 0.02761 0.40042 7.58621
25 5L2J 6UL 0.02968 0.40917 8.16327
26 1R6B ADP 0.01462 0.40175 8.27586
27 2Y6Q I7T 0.02834 0.40061 8.27586
28 5FCF GLY GLY GLY 0.01307 0.41479 8.96552
29 5BVE 4VG 0.03195 0.40514 9.65517
30 4F8L AES 0.04258 0.40167 9.65517
31 1I7A PHE 0.005582 0.42425 10.8108
32 1SBR VIB 0.0261 0.40129 11.7241
33 5KR7 6X9 0.00502 0.42825 12.4138
34 1JR8 FAD 0.002712 0.41988 13.6752
35 1HQS CIT 0.02534 0.40195 17.931
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