Receptor
PDB id Resolution Class Description Source Keywords
1DNP 2.3 Å EC: 4.1.99.3 STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE ESCHERICHIA COLI DNA REPAIR ELECTRON TRANSFER EXCITATION ENERGY TRANSFER LYASE CARBON-CARBON LYASE (CARBON-CARBON)
Ref.: CRYSTAL STRUCTURE OF DNA PHOTOLYASE FROM ESCHERICHIA COLI. SCIENCE V. 268 1866 1995
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAD A:472;
B:472;
Valid;
Valid;
none;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
MHF A:473;
B:473;
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
1DNP 2.3 Å EC: 4.1.99.3 STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE ESCHERICHIA COLI DNA REPAIR ELECTRON TRANSFER EXCITATION ENERGY TRANSFER LYASE CARBON-CARBON LYASE (CARBON-CARBON)
Ref.: CRYSTAL STRUCTURE OF DNA PHOTOLYASE FROM ESCHERICHIA COLI. SCIENCE V. 268 1866 1995
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1DNP - MHF C20 H23 N7 O6 c1cc(ccc1C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1DNP - MHF C20 H23 N7 O6 c1cc(ccc1C....
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 1OWM - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 1OWN - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 1OWL - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 1QNF - HDF C16 H17 N3 O7 c1cc2c(cc1....
5 1OWO - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 1OWP - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
7 1DNP - MHF C20 H23 N7 O6 c1cc(ccc1C....
8 1U3D Kd = 75 uM ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
9 4U63 - 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 : 1DNP; Ligand: FAD; Similar sites found: 45
This union binding pocket(no: 1) in the query (biounit: 1dnp.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.003743 0.45115 None
2 1N13 AG2 0.03515 0.40536 None
3 2QQC AG2 0.04309 0.40031 None
4 1SQK LAR 0.01661 0.41209 1.32626
5 2OCI TYC 0.02522 0.41181 1.9685
6 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.04871 0.40461 2.04082
7 5CQG 55C 0.02343 0.41324 2.54777
8 5GVR LMR 0.01675 0.40423 2.5641
9 2XN5 FUN 0.009985 0.42318 2.57143
10 4DJA FAD 0.0000000003778 0.50051 2.76008
11 4DJA DLZ 0.0000000003778 0.50051 2.76008
12 5TH5 MET 0.03534 0.40479 3.04183
13 5GQX GLC GLC GLC 0.03415 0.40754 3.18471
14 1TV5 N8E 0.03312 0.40466 3.386
15 5DXE EST 0.01844 0.40245 3.44828
16 5EXA 5SO 0.01204 0.42338 3.47826
17 5HYR EST 0.02001 0.40075 3.48837
18 5ICK FEZ 0.009827 0.40509 3.93013
19 2JCB ADP 0.00805 0.42786 4
20 2Z9I GLY ALA THR VAL 0.03194 0.40299 4.01235
21 3UEC ALA ARG TPO LYS 0.009723 0.43106 4.10959
22 1GXO ADA ADA ADA 0.01795 0.42282 4.21687
23 4DK7 0KS 0.003567 0.42477 4.45344
24 5UGW GSH 0.003151 0.44219 4.57143
25 1M2Z BOG 0.02797 0.41045 4.66926
26 5AVF TAU 0.03096 0.4022 4.66926
27 3FAL REA 0.01753 0.40351 4.95868
28 4YMU ARG 0.03091 0.40853 5
29 3SHZ 5CO 0.003134 0.44833 5.4755
30 3FC4 EDO 0.01671 0.40072 5.73248
31 2GC0 PAN 0.006175 0.41762 5.85106
32 1XX4 BAM 0.03678 0.40472 6.51341
33 4V3I ASP LEU THR ARG PRO 0.005377 0.45203 6.61479
34 4MRP GSH 0.03073 0.40381 6.79405
35 5UC9 MYR 0.02388 0.40805 7.07965
36 4S1D 41M 0.01199 0.42803 7.72727
37 1Y75 NAG 0.02182 0.41007 8.47458
38 1ZOY UQ1 0.04348 0.40044 11.4286
39 4KPM BEN 0.009763 0.42562 12.5
40 1NF8 BOG 0.01465 0.42895 17.8744
41 4UY1 TJM 0.01469 0.41477 19.8473
42 3PMA SCR 0.01042 0.43399 31.0345
43 4I6G FAD 0.00000000003088 0.72578 43.949
44 2J4D FAD 0.00000000000002809 0.83969 45.0106
45 4GU5 FAD 0.0000000000143 0.73354 48.4076
Pocket No.: 2; Query (leader) PDB : 1DNP; Ligand: MHF; Similar sites found: 67
This union binding pocket(no: 2) in the query (biounit: 1dnp.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1ZOA 140 0.02493 0.42379 1.27389
2 2CKM AA7 0.01985 0.42289 1.4862
3 2IYA UDP 0.02575 0.40457 1.65094
4 4L2H AR6 AR6 0.02043 0.43212 1.69851
5 2DTX BMA 0.01731 0.43851 1.89394
6 3K00 MTT 0.03381 0.41557 2.20049
7 1MO9 FAD 0.01875 0.45712 2.33546
8 2ZE7 DST 0.01719 0.42622 2.37154
9 4NCN GTP 0.01655 0.41667 2.407
10 4J7U YTZ 0.03062 0.42649 2.43056
11 4J7U NAP 0.03062 0.42649 2.43056
12 1MOQ GLP 0.01868 0.4155 2.44565
13 3H4T UDP 0.01063 0.42632 2.47525
14 1Z6Z NAP 0.01631 0.43061 2.48227
15 4RD0 GDP 0.001596 0.47471 2.6506
16 4D42 NAP 0.02453 0.44388 2.83688
17 4D42 W0I 0.02453 0.44388 2.83688
18 5O4J SAH 0.0189 0.4337 2.91971
19 5O4J 9KH 0.0189 0.4337 2.91971
20 5O4J PJL 0.02152 0.42847 2.91971
21 2FFQ GSP 0.01474 0.41932 2.92398
22 5I0H ADP BEF 0.00452 0.45375 2.9724
23 2VK4 TPP 0.0231 0.41463 2.9724
24 2GCO GNP 0.009243 0.4281 2.98507
25 1XX6 ADP 0.01136 0.4168 3.14136
26 2BME GNP 0.01916 0.41764 3.22581
27 1XTQ GDP 0.04802 0.40399 3.38983
28 4EN4 GT1 0.01757 0.43363 3.52564
29 4EN4 GT0 0.01757 0.43363 3.52564
30 4EN4 ATP 0.01757 0.43363 3.52564
31 2PD4 NAD 0.02393 0.42615 3.63636
32 2PD4 DCN 0.02586 0.42451 3.63636
33 1M2O GNP 0.01859 0.41401 3.68421
34 5SZH GNP 0.01058 0.4274 3.92157
35 2VCH UDP 0.01927 0.43603 4.03397
36 3V2U ATP 0.03119 0.40701 4.03397
37 2DT9 THR 0.01563 0.40746 4.19162
38 1QG6 NAD 0.02522 0.43839 4.21456
39 1QG6 TCL 0.02522 0.43839 4.21456
40 4PFW MAN MAN BMA BMA BMA BMA 0.01661 0.44631 4.24628
41 3R96 ACO 0.04698 0.41372 4.25532
42 3R96 AMP 0.04698 0.41372 4.25532
43 2VOH CIT 0.0115 0.41119 4.4586
44 4BAS GNP 0.02551 0.40347 4.52261
45 3HVJ 705 0.04794 0.40625 4.52489
46 3SIG AR6 0.009213 0.43567 4.69314
47 1OIX GDP 0.01402 0.43186 4.71204
48 2AOT SAH 0.02172 0.40112 4.79452
49 1VG8 GNP 0.025 0.40147 4.83092
50 3QKT ANP 0.02227 0.411 5.01475
51 2HV8 GTP 0.03337 0.41328 5.23256
52 1PJS NAD 0.02168 0.40076 5.25164
53 2XTZ GSP 0.01345 0.42491 5.36723
54 2D7C GTP 0.03236 0.41355 5.38922
55 1NFQ NAI 0.02871 0.41454 5.76923
56 2IXE ATP 0.02433 0.40722 6.36943
57 4C4P GNP 0.007049 0.44976 6.54206
58 2B8W ALF 5GP 0.02775 0.41896 7.0122
59 1LFD GNP 0.00586 0.43902 7.78443
60 1NVV GNP 0.01565 0.41152 7.83133
61 3WXM GTP 0.01682 0.41953 9.04255
62 2UZH CDP 0.03474 0.40242 12.1212
63 2ZAT NAP 0.03218 0.40951 14.6154
64 2QTV GNP 0.02606 0.40184 16.3265
65 1NF3 GNP 0.0198 0.40599 20.3125
66 2FAV APR 0.01261 0.4277 21.1111
67 2J4D MHF 0.001557 0.45114 45.0106
Pocket No.: 3; Query (leader) PDB : 1DNP; Ligand: FAD; Similar sites found: 16
This union binding pocket(no: 3) in the query (biounit: 1dnp.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3RV5 DXC 0.0009546 0.44606 None
2 5TME UDP 0.006476 0.434 1.49893
3 2D24 XYS XYS 0.03303 0.41239 1.6055
4 4LH7 NMN 0.0351 0.4065 2.78638
5 4KJG 4NP 0.03832 0.40202 3.18471
6 4UYF 73B 0.01853 0.41937 3.24675
7 1PZM 5GP 0.0239 0.40933 3.31754
8 4OJ8 AKG 0.008473 0.40615 3.41297
9 4MTI 2DX 0.03219 0.40659 3.47826
10 5HX1 UMP 0.04314 0.40067 5.7971
11 4K30 NLG 0.0179 0.41179 6.875
12 1IK4 PGH 0.02084 0.40473 7.23684
13 2YIP YIO 0.02231 0.41576 7.24638
14 2YKL NLD 0.02399 0.40171 8.01887
15 2Z77 NCA 0.03663 0.40358 10.7914
16 1SQL GUN 0.03415 0.40778 19.863
Pocket No.: 4; Query (leader) PDB : 1DNP; Ligand: MHF; Similar sites found: 8
This union binding pocket(no: 4) in the query (biounit: 1dnp.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZJ3 G6P 0.02517 0.40914 2.13333
2 1EDO NAP 0.02764 0.41863 2.45902
3 4KRI SAH 0.02 0.40161 3.00231
4 1WY7 SAH 0.04496 0.40105 3.38164
5 4WZA ACP 0.01214 0.45534 6.52174
6 2ED4 FAD 0.04429 0.4002 6.71141
7 3TNF GNP 0.01144 0.42272 7.47126
8 1TU3 GNP 0.01411 0.42774 12.6582
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