Receptor
PDB id Resolution Class Description Source Keywords
4CDN 1.9 Å EC: 4.1.99.3 CRYSTAL STRUCTURE OF M. MAZEI PHOTOLYASE WITH ITS IN VIVO RECONSTITUTED 8-HDF ANTENNA CHROMOPHORE METHANOSARCINA MAZEI LYASE PHOTOLYASE DNA REPAIR METHANOSARCINA MAZEI ANTENNACHROMOPHORE 8-HDF FAD
Ref.: STRUCTURAL AND EVOLUTIONARY ASPECTS OF ANTENNA CHRO USAGE BY CLASS II PHOTOLYASES. J.BIOL.CHEM. V. 289 19659 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PGE A:1467;
A:1469;
Invalid;
Invalid;
none;
none;
submit data
150.173 C6 H14 O4 C(COC...
FAD A:998;
B:998;
Valid;
Valid;
none;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
GOL A:1464;
B:1463;
A:1463;
A:1465;
B:1464;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PEG A:1470;
A:1471;
A:1468;
A:1472;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
FO1 A:999;
B:999;
Valid;
Valid;
none;
none;
submit data
363.322 C16 H17 N3 O7 c1cc2...
SO4 A:1466;
B:1466;
B:1465;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4CDN 1.9 Å EC: 4.1.99.3 CRYSTAL STRUCTURE OF M. MAZEI PHOTOLYASE WITH ITS IN VIVO RECONSTITUTED 8-HDF ANTENNA CHROMOPHORE METHANOSARCINA MAZEI LYASE PHOTOLYASE DNA REPAIR METHANOSARCINA MAZEI ANTENNACHROMOPHORE 8-HDF FAD
Ref.: STRUCTURAL AND EVOLUTIONARY ASPECTS OF ANTENNA CHRO USAGE BY CLASS II PHOTOLYASES. J.BIOL.CHEM. V. 289 19659 2014
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5O86 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5O8D - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 2XRY - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 4CDN - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 5O8E - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5O86 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5O8D - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 2XRY - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 4CDN - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 5O8E - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5O86 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5O8D - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 2XRY - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 4CDN - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 5O8E - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 3UMV - 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: FO1; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 FO1 1 1
2 HDF 1 1
3 F42 0.508333 0.833333
4 6J4 0.508333 0.833333
5 RBF 0.423913 0.871429
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4CDN; Ligand: FAD; Similar sites found: 29
This union binding pocket(no: 1) in the query (biounit: 4cdn.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2DKD NG1 0.02551 0.40786 1.45228
2 2YJP CYS 0.02981 0.40914 2.4055
3 4UTU LRY 0.02176 0.40031 2.62009
4 5AMC GLY NIY 0.02439 0.40887 2.6971
5 4FMS BDP 0.01971 0.41794 3.02267
6 4DK7 0KS 0.007388 0.41204 4.04858
7 5V4R MGT 0.0316 0.41122 4.32099
8 1AIQ CB3 0.02502 0.4008 4.54545
9 3KP6 SAL 0.03285 0.41213 4.63576
10 5ICK FEZ 0.01047 0.40523 4.80349
11 2EG5 SAH 0.02358 0.40207 5.91398
12 3BPX SAL 0.0315 0.40361 6.08108
13 2QQC AG2 0.03561 0.40617 6.25
14 1NF8 BOG 0.04119 0.40172 7.72947
15 4Q3S X7A 0.02027 0.40179 7.79221
16 2UVO NAG 0.01788 0.42912 8.18713
17 2UVO NDG 0.02386 0.41317 8.18713
18 4DJA FAD 0.0000000003453 0.50454 9.54357
19 4DJA DLZ 0.0000000003453 0.50454 9.54357
20 4GU5 FAD 0.000000003239 0.63442 10.5809
21 2Z77 NCA 0.04164 0.40059 10.7914
22 3B6C SDN 0.01272 0.42803 11.1111
23 4U63 FAD 0.00000000000481 0.74339 13.9004
24 2XCM ADP 0.006607 0.42519 16.3043
25 2CB8 MYA 0.02418 0.41422 18.3908
26 1U3D FAD 0.000000000005469 0.74124 29.2531
27 2J4D FAD 0.00000000003745 0.70905 30.083
28 4I6G FAD 0.000000006101 0.63725 30.2905
29 1NP7 FAD 0.00000000001433 0.72512 31.9502
Pocket No.: 2; Query (leader) PDB : 4CDN; Ligand: FO1; Similar sites found: 20
This union binding pocket(no: 2) in the query (biounit: 4cdn.bio1) has 48 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4FMS BDP 0.04265 0.41794 3.02267
2 3W54 RNB 0.01525 0.42697 3.34347
3 4MN7 SME 0.02345 0.42453 4.02685
4 4DK7 0KS 0.01942 0.41204 4.04858
5 5ICK FEZ 0.02508 0.40669 4.80349
6 5KAX RHQ 0.02726 0.42892 7.22892
7 4Q3S X7A 0.04711 0.40179 7.79221
8 2UVO NAG 0.03539 0.42941 8.18713
9 2UVO NDG 0.04241 0.41467 8.18713
10 4Q9M 2ZW 0.02284 0.40582 8.53659
11 5U9J GER 0.04285 0.41782 8.87574
12 4DJA DLZ 0.000000001947 0.56728 9.54357
13 4DJA FAD 0.000000001947 0.56728 9.54357
14 4GU5 FAD 0.00000002765 0.47502 10.5809
15 4U63 FAD 0.00000000006284 0.53683 13.9004
16 2XCM ADP 0.02303 0.41781 16.3043
17 1U3D FAD 0.000000000073 0.5364 29.2531
18 2J4D FAD 0.0000000004203 0.51696 30.083
19 4I6G FAD 0.00000004656 0.63725 30.2905
20 1NP7 FAD 0.0000000001789 0.52662 31.9502
Pocket No.: 3; Query (leader) PDB : 4CDN; Ligand: FAD; Similar sites found: 4
This union binding pocket(no: 3) in the query (biounit: 4cdn.bio2) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3W54 RNB 0.005146 0.42267 3.34347
2 3PLN U5P 0.04171 0.40055 4.95283
3 5KAX RHQ 0.01232 0.42876 7.22892
4 5OCA 9QZ 0.03287 0.41208 12.1849
Pocket No.: 4; Query (leader) PDB : 4CDN; Ligand: FO1; Similar sites found: 6
This union binding pocket(no: 4) in the query (biounit: 4cdn.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4Z24 FAD 0.02801 0.40035 2.07469
2 3DGY 2GP 0.0259 0.40188 5.15464
3 4COQ SAN 0.02875 0.40208 6.07287
4 2GTE VA 0.009941 0.40042 7.25806
5 5XVQ 8GC 0.02148 0.40577 7.39437
6 1UPR 4IP 0.03124 0.40808 12.1951
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