Receptor
PDB id Resolution Class Description Source Keywords
4DJA 1.45 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF A PROKARYOTIC (6-4) PHOTOLYASE PHRB FRO AGROBACTERIUM TUMEFACIENS WITH AN FE-S CLUSTER AND A 6,7-DIR IBITYLLUMAZINE ANTENNA CHROMOPHORE AT 1.45A RESOLUTION AGROBACTERIUM TUMEFACIENS PHOTOLYASE DNA REPAIR LYASE IRON-SULFUR CLUSTER FLAVOPRO
Ref.: CRYSTAL STRUCTURE OF A PROKARYOTIC (6-4) PHOTOLYASE FE-S CLUSTER AND A 6,7-DIMETHYL-8-RIBITYLLUMAZINE A CHROMOPHORE. PROC.NATL.ACAD.SCI.USA V. 110 7217 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DLZ A:602;
Valid;
none;
submit data
326.305 C13 H18 N4 O6 CC1=C...
SF4 A:603;
Part of Protein;
none;
submit data
351.64 Fe4 S4 [S]12...
GOL A:606;
A:605;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NA A:604;
Part of Protein;
none;
submit data
22.99 Na [Na+]
FAD A:601;
Valid;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DJA 1.45 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF A PROKARYOTIC (6-4) PHOTOLYASE PHRB FRO AGROBACTERIUM TUMEFACIENS WITH AN FE-S CLUSTER AND A 6,7-DIR IBITYLLUMAZINE ANTENNA CHROMOPHORE AT 1.45A RESOLUTION AGROBACTERIUM TUMEFACIENS PHOTOLYASE DNA REPAIR LYASE IRON-SULFUR CLUSTER FLAVOPRO
Ref.: CRYSTAL STRUCTURE OF A PROKARYOTIC (6-4) PHOTOLYASE FE-S CLUSTER AND A 6,7-DIMETHYL-8-RIBITYLLUMAZINE A CHROMOPHORE. PROC.NATL.ACAD.SCI.USA V. 110 7217 2013
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 38 families.
1 5LFA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5KCM - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 4DJA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 5LFA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5KCM - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 4DJA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 5LFA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5KCM - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 4DJA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DLZ; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 DLZ 1 1
2 1VY 0.698413 0.955882
3 RBF 0.546667 0.885714
4 RLP 0.506494 0.887324
5 RS3 0.506173 0.837838
6 FMN 0.404494 0.782051
Ligand no: 2; 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DJA; Ligand: FAD; Similar sites found: 19
This union binding pocket(no: 1) in the query (biounit: 4dja.bio1) has 51 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4XH0 ADP 0.04536 0.4194 2.23325
2 3ZJQ NCA 0.03585 0.40645 2.5641
3 4GU5 FAD 0.000000006334 0.47671 2.7027
4 1DNP FAD 0.0000000003778 0.50051 2.76008
5 4XNV BUR 0.04574 0.41999 3.08789
6 3Q3H UDP 0.03608 0.42423 4.2471
7 1QNF FAD 0.0000000004218 0.71463 4.54545
8 1QNF HDF 0.0000000007752 0.59595 4.54545
9 4N39 UDP 0.03821 0.40563 4.6332
10 3KP6 SAL 0.009921 0.46091 5.29801
11 1GEG GLC 0.01622 0.42538 8.59375
12 4CDN FO1 0.000000001947 0.56728 9.54357
13 4CDN FAD 0.0000000003453 0.50454 9.54357
14 3UMV FAD 0.000000001598 0.48454 10.4743
15 5EQ0 5R0 PHE ALA LEU ELY 5R5 0.02888 0.41181 10.9091
16 2J4D FAD 0.000000001414 0.49348 11.583
17 2J07 HDF 0.0001684 0.45533 15.9524
18 2J07 FAD 0.0001684 0.45533 15.9524
19 1U3D FAD 0.0000000006528 0.50358 18.2711
Pocket No.: 2; Query (leader) PDB : 4DJA; Ligand: DLZ; Similar sites found: 19
This union binding pocket(no: 2) in the query (biounit: 4dja.bio1) has 51 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4XH0 ADP 0.04536 0.4194 2.23325
2 3ZJQ NCA 0.03585 0.40645 2.5641
3 4GU5 FAD 0.000000006334 0.47671 2.7027
4 1DNP FAD 0.0000000003778 0.50051 2.76008
5 4XNV BUR 0.04574 0.41999 3.08789
6 3Q3H UDP 0.03608 0.42423 4.2471
7 1QNF FAD 0.0000000004218 0.71463 4.54545
8 1QNF HDF 0.0000000007752 0.59595 4.54545
9 4N39 UDP 0.03821 0.40563 4.6332
10 3KP6 SAL 0.009921 0.46091 5.29801
11 1GEG GLC 0.01622 0.42538 8.59375
12 4CDN FO1 0.000000001947 0.56728 9.54357
13 4CDN FAD 0.0000000003453 0.50454 9.54357
14 3UMV FAD 0.000000001598 0.48454 10.4743
15 5EQ0 5R0 PHE ALA LEU ELY 5R5 0.02888 0.41181 10.9091
16 2J4D FAD 0.000000001414 0.49348 11.583
17 2J07 HDF 0.0001684 0.45533 15.9524
18 2J07 FAD 0.0001684 0.45533 15.9524
19 1U3D FAD 0.0000000006528 0.50358 18.2711
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