Receptor
PDB id Resolution Class Description Source Keywords
3HBF 2.1 Å EC: 2.4.1.- STRUCTURE OF UGT78G1 COMPLEXED WITH MYRICETIN AND UDP MEDICAGO TRUNCATULA GLYCOSYLTRANSFERASE GT-B FOLD GT1 PHENYLPROPANOID METABOLISM TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF GLYCOSYLTRANSFERASE UGT78G1 REVEAL THE MOLECULAR BASIS FOR GLYCOSYLATION AND DEGLYCOSYLATION OF (ISO)FLAVONOIDS. J.MOL.BIOL. V. 392 1292 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MYC A:901;
Valid;
none;
submit data
318.235 C15 H10 O8 c1c(c...
UDP A:900;
Valid;
none;
submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3HBF 2.1 Å EC: 2.4.1.- STRUCTURE OF UGT78G1 COMPLEXED WITH MYRICETIN AND UDP MEDICAGO TRUNCATULA GLYCOSYLTRANSFERASE GT-B FOLD GT1 PHENYLPROPANOID METABOLISM TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF GLYCOSYLTRANSFERASE UGT78G1 REVEAL THE MOLECULAR BASIS FOR GLYCOSYLATION AND DEGLYCOSYLATION OF (ISO)FLAVONOIDS. J.MOL.BIOL. V. 392 1292 2009
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 3HBF - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 3HBJ - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 3HBF - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 3HBJ - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4REL - KMP C15 H10 O6 c1cc(ccc1C....
2 4WHM - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
3 3HBF - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
4 3HBJ - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
5 2C1X - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 2C9Z - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
7 2C1Z - U2F C15 H23 F N2 O16 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MYC; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 MYC 1 1
2 QUE 0.649123 1
3 KMP 0.642857 0.967742
4 MRI 0.55 0.967742
5 CC6 0.507937 0.967742
Ligand no: 2; Ligand: UDP; Similar ligands found: 116
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 UNP 0.8 0.970149
4 U5P 0.78125 0.984615
5 UPU 0.72973 0.940298
6 2KH 0.722222 0.970149
7 44P 0.720588 0.955882
8 URM 0.717949 0.927536
9 GUD 0.717949 0.941176
10 GDU 0.717949 0.941176
11 UFM 0.717949 0.941176
12 UPG 0.717949 0.941176
13 660 0.717949 0.927536
14 UDP UDP 0.714286 0.939394
15 UDH 0.705128 0.864865
16 UPP 0.705128 0.941176
17 UPF 0.691358 0.888889
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UDX 0.670732 0.941176
21 UAD 0.670732 0.941176
22 3UC 0.658824 0.888889
23 USQ 0.654762 0.820513
24 UGB 0.654762 0.955224
25 UGA 0.654762 0.955224
26 G3N 0.647059 0.914286
27 UDM 0.636364 0.914286
28 URI 0.625 0.863636
29 U 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 UDP GAL 0.611765 0.913043
33 Y6W 0.607143 0.888889
34 CDP 0.605263 0.942029
35 UD7 0.591398 0.927536
36 HP7 0.591398 0.941176
37 MJZ 0.585106 0.914286
38 IUG 0.583333 0.810127
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 UD4 0.578947 0.914286
42 CJB 0.573529 0.820895
43 UDZ 0.571429 0.853333
44 DUD 0.571429 0.913043
45 UP5 0.571429 0.853333
46 U U 0.563218 0.955224
47 EPZ 0.56 0.914286
48 5GW 0.559524 0.942029
49 EPU 0.554455 0.901408
50 EEB 0.554455 0.901408
51 UA3 0.547945 0.939394
52 U3P 0.547945 0.939394
53 CH 0.546667 0.913043
54 4TC 0.544554 0.831169
55 CTP 0.54321 0.942029
56 CSV 0.531915 0.851351
57 CSQ 0.531915 0.851351
58 DUT 0.52439 0.913043
59 4GW 0.516484 0.915493
60 UMA 0.513761 0.914286
61 U4S 0.513158 0.753425
62 U2P 0.506667 0.954545
63 U2S 0.5 0.767123
64 U3S 0.5 0.753425
65 PUP 0.48913 0.913043
66 U22 0.486957 0.790123
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 DKX 0.486486 0.746479
70 U1S 0.482759 0.75
71 A U 0.481132 0.805195
72 2QR 0.478632 0.822785
73 5FU 0.474359 0.914286
74 8OD 0.47191 0.851351
75 C5G 0.468085 0.888889
76 7XL 0.465909 0.888889
77 U U U U 0.461538 0.940298
78 UMF 0.461538 0.857143
79 G8D 0.460674 0.855263
80 UTP U U U 0.456522 0.895522
81 2TU 0.452055 0.774648
82 4RA 0.451613 0.855263
83 C2G 0.450549 0.901408
84 DU 0.45 0.898551
85 CAR 0.45 0.927536
86 C 0.45 0.927536
87 C5P 0.45 0.927536
88 UMP 0.45 0.898551
89 UAG 0.448 0.864865
90 CDC 0.446809 0.777778
91 UD0 0.444444 0.844156
92 5BU 0.444444 0.914286
93 N3E 0.440476 0.733333
94 UC5 0.440476 0.9
95 UUA 0.438356 0.772727
96 DUP 0.431818 0.887324
97 2GW 0.431373 0.901408
98 M7G 0.430108 0.780488
99 CNU 0.428571 0.927536
100 CDM 0.427083 0.842105
101 H6Y 0.425532 0.851351
102 16B 0.421687 0.888889
103 S5P 0.419753 0.915493
104 8GT 0.419355 0.855263
105 CXY 0.418367 0.888889
106 UPA 0.418182 0.842105
107 CDP MG 0.413793 0.849315
108 U2G 0.410714 0.822785
109 U A A U 0.409836 0.842105
110 UML 0.408759 0.810127
111 UP6 0.407407 0.871429
112 M7M 0.40625 0.771084
113 PMP UD1 0.404762 0.794872
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3HBF; Ligand: UDP; Similar sites found: 44
This union binding pocket(no: 1) in the query (biounit: 3hbf.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5ENZ UDP 0.002798 0.42308 1.81818
2 2AWN ADP 0.01055 0.4281 2.09974
3 1T9D P22 0.02076 0.40642 2.20264
4 3WMX THR 0.001482 0.44069 2.23464
5 1P7T PYR 0.01179 0.42415 2.64317
6 1D8C GLV 0.0209 0.41941 2.64317
7 1U72 NDP 0.01049 0.42414 2.68817
8 5FJJ MAN 0.01125 0.40073 2.86344
9 3ITJ CIT 0.007851 0.44351 3.25444
10 4X1T UDP 0.00001965 0.48682 3.30396
11 2WPF WPF 0.03058 0.42269 3.52423
12 4PPF FLC 0.043 0.40384 3.71429
13 4X7R UDP 0.003104 0.4173 4.18502
14 2VOH CIT 0.01299 0.4312 4.4586
15 3B6C SDN 0.02172 0.4054 4.70085
16 4WZ6 ATP 0.02828 0.40129 4.82759
17 2W47 UNF 0.01463 0.41576 4.86111
18 3NHB ADP 0.02064 0.40838 4.90196
19 3CV2 OXL 0.01456 0.42299 5.07519
20 3S2U UD1 0.0001223 0.46563 5.20548
21 1RRV TYD 0.0007385 0.44862 5.28846
22 2BL9 CP6 0.008901 0.41483 5.46218
23 2BL9 NDP 0.008901 0.41483 5.46218
24 2W9S NDP 0.009219 0.40454 6.21118
25 3H4T UDP 0.0001966 0.46658 6.68317
26 4QB6 GCU XYP 0.02106 0.41844 6.70732
27 1U70 NDP 0.005247 0.43233 8.06452
28 3HBN UDP 0.002654 0.40882 8.15603
29 2NUN ADP 0.005594 0.43064 8.35913
30 3OTI TYD 0.000009471 0.51072 8.79397
31 5BNW 12V 0.01493 0.40137 9.03084
32 4RIF 3R2 0.00002206 0.51771 10.2902
33 3IAA TYD 0.000005676 0.52949 10.8173
34 3RSC TYD 0.000004343 0.53701 10.8434
35 3Q3H UDP 0.007757 0.42838 11.2335
36 4LAE NAP 0.0141 0.41728 11.976
37 4LAE 1VM 0.0141 0.41728 11.976
38 2FZH DH1 0.01343 0.41157 13.1068
39 4M7V RAR 0.01253 0.41476 14.8571
40 1DR1 NAP 0.00511 0.42687 17.9894
41 1DR1 HBI 0.00511 0.42687 17.9894
42 3OTH TYD 0.0000003699 0.60213 23.0583
43 3OTH CLJ 0.000003258 0.41035 23.0583
44 2VCH UDP 0.0000000007843 0.71481 47.1366
Pocket No.: 2; Query (leader) PDB : 3HBF; Ligand: MYC; Similar sites found: 36
This union binding pocket(no: 2) in the query (biounit: 3hbf.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3WCS MAN NAG 0.04728 0.40425 1.5748
2 2AWN ADP 0.01686 0.43231 2.09974
3 1T9D P22 0.03976 0.40839 2.20264
4 2B6N ALA PRO THR 0.04302 0.40265 2.20264
5 3WMX THR 0.002787 0.46031 2.23464
6 1P7T PYR 0.02283 0.42415 2.64317
7 1D8C GLV 0.03846 0.41941 2.64317
8 5FJJ MAN 0.02027 0.40073 2.86344
9 2OG2 MLI 0.04259 0.40869 3.06407
10 3ITJ CIT 0.000808 0.49613 3.25444
11 4X7R UDP 0.008021 0.41791 4.18502
12 2VOH CIT 0.02148 0.43316 4.4586
13 2BKX F6R 0.03006 0.40037 4.54545
14 4WZ6 ATP 0.03714 0.41182 4.82759
15 3NHB ADP 0.03637 0.41155 4.90196
16 2ILZ GTP 0.03607 0.40678 5.06608
17 3CV2 OXL 0.02742 0.42374 5.07519
18 3S2U UD1 0.0003427 0.47204 5.20548
19 1RRV TYD 0.002227 0.44741 5.28846
20 1GXU 2HP 0.02647 0.44182 5.49451
21 4A9C B5F 0.0421 0.405 5.6962
22 3W9F I3P 0.03547 0.40164 6.15385
23 3H4T UDP 0.00007113 0.40918 6.68317
24 1G6H ADP 0.04639 0.40942 7.393
25 2NUN ADP 0.01246 0.43123 8.35913
26 3OTI TYD 0.00004871 0.50941 8.79397
27 1JJ7 ADP 0.02591 0.41498 9.61539
28 4RIF 3R2 0.0001884 0.41695 10.2902
29 3IAA TYD 0.00002441 0.42046 10.8173
30 3RSC TYD 0.00001187 0.43424 10.8434
31 4B9E FAH 0.01992 0.43251 10.9635
32 3Q3H UDP 0.01853 0.42644 11.2335
33 3B5J 12D 0.04867 0.40356 12.3457
34 3OTH TYD 0.000001574 0.60213 23.0583
35 3OTH CLJ 0.0000168 0.44594 23.0583
36 2VCH UDP 0.00000001598 0.55497 47.1366
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