Receptor
PDB id Resolution Class Description Source Keywords
4U63 1.67 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF A BACTERIAL CLASS III PHOTOLYASE FROM AGROBACTERIUM TUMEFACIENS AT 1.67A RESOLUTION AGROBACTERIUM TUMEFACIENS PHOTOLYASE DNA REPAIR LYASE METHENYLTETRAHYDROFOLATE CYCLOPYRIMIDINE DIMER FLAVIN FAD FLAVOPROTEIN PHOTOREDUTRP TRIADE DOUBLE-STRANDED DNA DAMAGE DNA ULTRAVIOLET RAGROBACTERIUM TUMEFACIENS
Ref.: THE CLASS III CYCLOBUTANE PYRIMIDINE DIMER PHOTOLYA STRUCTURE REVEALS A NEW ANTENNA CHROMOPHORE BINDING ALTERNATIVE PHOTOREDUCTION PATHWAYS. J.BIOL.CHEM. V. 290 11504 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:1008;
A:1009;
A:1012;
A:1010;
A:1013;
A:1016;
A:1015;
A:1004;
A:1014;
A:1003;
A:1006;
A:1005;
A:1007;
A:1011;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
TRS A:1017;
Invalid;
none;
submit data
122.143 C4 H12 N O3 C(C(C...
FAD A:1002;
Valid;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
MHF A:1001;
Valid;
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
4U63 1.67 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF A BACTERIAL CLASS III PHOTOLYASE FROM AGROBACTERIUM TUMEFACIENS AT 1.67A RESOLUTION AGROBACTERIUM TUMEFACIENS PHOTOLYASE DNA REPAIR LYASE METHENYLTETRAHYDROFOLATE CYCLOPYRIMIDINE DIMER FLAVIN FAD FLAVOPROTEIN PHOTOREDUTRP TRIADE DOUBLE-STRANDED DNA DAMAGE DNA ULTRAVIOLET RAGROBACTERIUM TUMEFACIENS
Ref.: THE CLASS III CYCLOBUTANE PYRIMIDINE DIMER PHOTOLYA STRUCTURE REVEALS A NEW ANTENNA CHROMOPHORE BINDING ALTERNATIVE PHOTOREDUCTION PATHWAYS. J.BIOL.CHEM. V. 290 11504 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 38 families.
1 4U63 - FAD C27 H33 N9 O15 P2 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 35 families.
1 4U63 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
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 : 4U63; Ligand: FAD; Similar sites found: 54
This union binding pocket(no: 1) in the query (biounit: 4u63.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.0312 0.40087 None
2 4NS0 PIO 0.03934 0.40034 None
3 4V3I ASP LEU THR ARG PRO 0.008793 0.43979 1.55642
4 1J78 VDY 0.02415 0.40909 1.74672
5 3Q3H UDP 0.03419 0.40518 1.80723
6 1XMY ROL 0.03354 0.40167 2.01005
7 4LH7 NMN 0.04449 0.40039 2.16718
8 4UY1 TJM 0.01007 0.42436 2.29008
9 3SHZ 5CO 0.01066 0.42312 2.30548
10 5FPN KYD 0.02361 0.42486 2.40964
11 2GEK GDP 0.0213 0.40426 2.46305
12 1GQ2 OXL 0.02128 0.41838 3.01205
13 3MA0 XYP 0.03505 0.4046 3.19489
14 4ETZ C2E 0.02581 0.4076 3.367
15 5TH5 MET 0.02924 0.40982 3.42205
16 3PMA SCR 0.03147 0.41163 3.4749
17 1GY8 UDP 0.01873 0.41079 3.52645
18 5UC9 MYR 0.02323 0.41699 3.53982
19 5TDF ADE 0.002484 0.40848 3.7037
20 2Y9G LBT 0.01887 0.41841 4
21 2Y9G LAT 0.01887 0.41841 4
22 2X8S AHR AHR AHR 0.03645 0.40369 4.04255
23 1KKR 2AS 0.02794 0.41066 4.11622
24 2OYH GLY HIS ARG PRO 0.03651 0.40365 4.15335
25 3HW5 AMP 0.02623 0.41372 4.21456
26 5UGW GSH 0.001124 0.47957 4.57143
27 3TW1 AHN 0.039 0.40406 4.64135
28 5FYR INS 0.01342 0.42352 4.69799
29 1TV5 N8E 0.01334 0.43268 4.74041
30 5IQT AKG 0.007731 0.40791 5.07937
31 1WOG 16D 0.04402 0.40724 5.2459
32 2J1E NDG GAL 0.03453 0.40186 5.33333
33 1ZOY UQ1 0.01996 0.42096 5.82524
34 3WUR O4B 0.02966 0.41511 5.84795
35 5N1X 8HH 0.000008126 0.41542 5.9322
36 2BLF MSS 0.01161 0.40012 6.17284
37 3TK1 GDP 0.02866 0.40928 6.36364
38 2BP1 FLC 0.034 0.40132 6.38889
39 5DKK FMN 0.009681 0.40676 6.89655
40 5EW0 3C7 0.03182 0.40685 7.26496
41 2GC0 PAN 0.01272 0.40462 7.44681
42 3FAL REA 0.01672 0.41329 7.89474
43 1QY8 RDI 0.01453 0.40527 9.29368
44 2XN5 FUN 0.0155 0.41494 10.5714
45 4WGF HX2 0.0118 0.4182 10.7317
46 4YH2 GSH 0.02212 0.41107 10.8108
47 1V2A GTS 0.03495 0.40599 10.9524
48 4CDN FAD 0.00000000000481 0.74339 13.9004
49 4CDN FO1 0.00000000006284 0.53683 13.9004
50 4FLP JQ1 0.006076 0.44707 14.2857
51 4IBF 1D5 0.01431 0.40908 16.2791
52 3UMV FAD 0.000000000009094 0.74124 19.5652
53 2J4D FAD 0.000000000000001443 0.87914 41.9679
54 4GU5 FAD 0.000000000001514 0.76273 46.7871
Pocket No.: 2; Query (leader) PDB : 4U63; Ligand: MHF; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4u63.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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