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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 26 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 23 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 1 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: 117
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 U 0.78125 0.984615
6 UPU 0.72973 0.940298
7 2KH 0.722222 0.970149
8 44P 0.720588 0.955882
9 UFM 0.717949 0.941176
10 GDU 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GUD 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UPP 0.705128 0.941176
17 UDH 0.705128 0.864865
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UPF 0.691358 0.888889
21 UAD 0.670732 0.941176
22 UDX 0.670732 0.941176
23 3UC 0.658824 0.888889
24 USQ 0.654762 0.820513
25 UGB 0.654762 0.955224
26 UGA 0.654762 0.955224
27 G3N 0.647059 0.914286
28 UDM 0.636364 0.914286
29 URI 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 Y6W 0.607143 0.888889
33 CDP 0.605263 0.942029
34 HP7 0.591398 0.941176
35 UD7 0.591398 0.927536
36 MJZ 0.585106 0.914286
37 IUG 0.583333 0.810127
38 F5G 0.578947 0.927536
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 F5P 0.578947 0.914286
42 UD4 0.578947 0.914286
43 CJB 0.573529 0.820895
44 UDZ 0.571429 0.853333
45 DUD 0.571429 0.913043
46 UP5 0.571429 0.853333
47 U U 0.563218 0.955224
48 EPZ 0.56 0.914286
49 5GW 0.559524 0.942029
50 EPU 0.554455 0.901408
51 EEB 0.554455 0.901408
52 U3P 0.547945 0.939394
53 UA3 0.547945 0.939394
54 4TC 0.544554 0.831169
55 HF4 0.54321 0.942029
56 CTP 0.54321 0.942029
57 CSQ 0.531915 0.851351
58 CSV 0.531915 0.851351
59 DUT 0.52439 0.913043
60 4GW 0.516484 0.915493
61 UMA 0.513761 0.914286
62 U4S 0.513158 0.753425
63 U2P 0.506667 0.954545
64 U2S 0.5 0.767123
65 U3S 0.5 0.753425
66 PUP 0.48913 0.913043
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 U22 0.486957 0.790123
70 DKX 0.486486 0.746479
71 U1S 0.482759 0.75
72 A U 0.481132 0.805195
73 2QR 0.478632 0.822785
74 5FU 0.474359 0.914286
75 G U 0.472222 0.7875
76 8OD 0.47191 0.851351
77 C5G 0.468085 0.888889
78 7XL 0.465909 0.888889
79 U U U U 0.461538 0.940298
80 UMF 0.461538 0.857143
81 G8D 0.460674 0.855263
82 UTP U U U 0.456522 0.895522
83 2TU 0.452055 0.774648
84 4RA 0.451613 0.855263
85 C2G 0.450549 0.901408
86 DU 0.45 0.898551
87 UMP 0.45 0.898551
88 C 0.45 0.927536
89 CAR 0.45 0.927536
90 C5P 0.45 0.927536
91 UAG 0.448 0.864865
92 CDC 0.446809 0.777778
93 5BU 0.444444 0.914286
94 UD0 0.444444 0.844156
95 N3E 0.440476 0.733333
96 UC5 0.440476 0.9
97 UUA 0.438356 0.772727
98 DUP 0.431818 0.887324
99 2GW 0.431373 0.901408
100 M7G 0.430108 0.780488
101 CNU 0.428571 0.927536
102 CDM 0.427083 0.842105
103 H6Y 0.425532 0.851351
104 16B 0.421687 0.888889
105 S5P 0.419753 0.915493
106 8GT 0.419355 0.855263
107 CXY 0.418367 0.888889
108 UPA 0.418182 0.842105
109 U2G 0.410714 0.822785
110 U A A U 0.409836 0.842105
111 UML 0.408759 0.810127
112 UP6 0.407407 0.871429
113 M7M 0.40625 0.771084
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
117 PMP UD1 0.401575 0.7875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3HBF; Ligand: UDP; Similar sites found with APoc: 102
This union binding pocket(no: 1) in the query (biounit: 3hbf.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 3KPE TM3 None
2 5NM7 GLY 1.50376
3 5ENZ UDP 1.81818
4 3IA4 NDP 1.85185
5 2AWN ADP 2.09974
6 5AJU RP5 2.18978
7 1YQT ADP 2.20264
8 5YV5 ADP 2.20264
9 1T9D P22 2.20264
10 4DP3 MMV 2.20264
11 4DP3 NDP 2.20264
12 5WKC TP9 2.20264
13 3WMX THR 2.23464
14 5W8X UDP 2.35602
15 5YAP NAI 2.36842
16 5YAP 8S0 2.36842
17 5GQI CTP 2.42915
18 2PZE ATP 2.62009
19 1P7T PYR 2.64317
20 1D8C GLV 2.64317
21 1U72 NDP 2.68817
22 1U72 MTX 2.68817
23 2D2F ADP 2.8
24 5FJJ MAN 2.86344
25 3NRR NAP 3.0837
26 3NRR D16 3.0837
27 1Q19 SSC 3.0837
28 1BZL GCG 3.0837
29 3ITJ CIT 3.25444
30 4X1T UDP 3.30396
31 2WPF FAD 3.52423
32 2WPF WPF 3.52423
33 4U00 ADP 3.68852
34 4PPF FLC 3.71429
35 5IFK HPA 3.84615
36 5URY PAM 4.10959
37 4HE2 AMP 4.14201
38 4X7R UDP 4.18502
39 4X7R NTO 4.18502
40 4X7R 3YW 4.18502
41 4WBD CIT 4.40529
42 2VOH CIT 4.4586
43 2XN2 GLA 4.5082
44 6F5W KG1 4.60705
45 3B6C SDN 4.70085
46 4RM0 FUC NDG GAL 4.74684
47 4WZ6 ATP 4.82759
48 2W47 UNF 4.86111
49 3NHB ADP 4.90196
50 5GLN XYP XYP XYP 4.94186
51 3CV2 OXL 5.07519
52 2F7C CCU 5.15021
53 4USI AKG 5.19481
54 3S2U UD1 5.20548
55 4G86 BNT 5.28169
56 1RRV TYD 5.28846
57 2BL9 NDP 5.46218
58 2BL9 CP6 5.46218
59 1J3I NDP 5.4878
60 1CY2 TMP 5.50661
61 4KVL PLM 5.63607
62 2ZJ5 ADP 5.94714
63 2W9S NDP 6.21118
64 1AOE GW3 6.25
65 1AOE NDP 6.25
66 2VWT PYR 6.36704
67 3BEO UDP 6.4
68 3H4T UDP 6.68317
69 4QB6 GCU XYP 6.70732
70 5W6Y TRP 6.96203
71 1O8B ABF 7.30594
72 1MVN PCO 7.6555
73 1MVN FMN 7.6555
74 2P39 SCR 7.74194
75 1JT2 FER 7.83582
76 1U70 NDP 8.06452
77 1U70 MTX 8.06452
78 3HBN UDP 8.15603
79 5E5U MLI 8.33333
80 2NUN ADP 8.35913
81 3OTI TYD 8.79397
82 5BNW 12V 9.03084
83 2FWP ICR 9.28962
84 4EIL NDP 9.47137
85 3EEL 53T 9.69163
86 4RIF 3R2 10.2902
87 4NTO 1PW 10.628
88 3IAA TYD 10.8173
89 3RSC TYD 10.8434
90 3Q3H UDP 11.2335
91 4LAE NAP 11.976
92 4LAE 1VM 11.976
93 2FZH DH1 13.1068
94 3KP6 SAL 13.245
95 1GZF NIR 13.2701
96 4M7V RAR 14.8571
97 1M0S CIT 15.9817
98 1DR1 HBI 17.9894
99 1DR1 NAP 17.9894
100 3OTH CLJ 23.0583
101 3OTH TYD 23.0583
102 2VCH UDP 47.1366
Pocket No.: 2; Query (leader) PDB : 3HBF; Ligand: MYC; Similar sites found with APoc: 78
This union binding pocket(no: 2) in the query (biounit: 3hbf.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 3KPE TM3 None
2 5NM7 GLY 1.50376
3 3WCS MAN NAG 1.5748
4 3L6R MLI 2.02312
5 2AWN ADP 2.09974
6 5AJU RP5 2.18978
7 1YQT ADP 2.20264
8 5YV5 ADP 2.20264
9 1T9D P22 2.20264
10 5WKC TP9 2.20264
11 2B6N ALA PRO THR 2.20264
12 3WMX THR 2.23464
13 5W8X UDP 2.35602
14 2NZ2 ASP 2.42131
15 2GKS ADP 2.42291
16 5GQI CTP 2.42915
17 2PZE ATP 2.62009
18 1P7T PYR 2.64317
19 1D8C GLV 2.64317
20 1VAY AZA 2.78746
21 2D2F ADP 2.8
22 5FJJ MAN 2.86344
23 3WLV AZA 2.88462
24 2OG2 MLI 3.06407
25 1Q19 SSC 3.0837
26 5ZXD ATP 3.0837
27 3ITJ CIT 3.25444
28 4X1T UDP 3.30396
29 4U00 ADP 3.68852
30 5IFK HPA 3.84615
31 5URY PAM 4.10959
32 2EFX NFA 4.13223
33 4X7R UDP 4.18502
34 4WBD CIT 4.40529
35 2VOH CIT 4.4586
36 2BKX F6R 4.54545
37 4RM0 FUC NDG GAL 4.74684
38 4WZ6 ATP 4.82759
39 3NHB ADP 4.90196
40 5GLN XYP XYP XYP 4.94186
41 3CV2 OXL 5.07519
42 2F7C CCU 5.15021
43 4USI AKG 5.19481
44 3S2U UD1 5.20548
45 4G86 BNT 5.28169
46 1RRV TYD 5.28846
47 3CYI ATP 5.45455
48 1GXU 2HP 5.49451
49 1CY2 TMP 5.50661
50 4KVL PLM 5.63607
51 4A9C B5F 5.6962
52 2BOS GLA GAL GLC NBU 5.88235
53 2ZJ5 ADP 5.94714
54 3W9F I3P 6.15385
55 4D1J DGJ 6.48148
56 3H4T UDP 6.68317
57 1G6H ADP 7.393
58 1P0Z FLC 7.63359
59 2P39 SCR 7.74194
60 4JLS 3ZE 7.89474
61 3HBN UDP 8.15603
62 5E5U MLI 8.33333
63 2NUN ADP 8.35913
64 3OTI TYD 8.79397
65 4HZ0 1AV 8.92019
66 1JJ7 ADP 9.61539
67 4RIF 3R2 10.2902
68 4NTO 1PW 10.628
69 3IAA TYD 10.8173
70 3RSC TYD 10.8434
71 4B9E FAH 10.9635
72 1FWV SGA MAG FUC 11.194
73 3Q3H UDP 11.2335
74 3B5J 12D 12.3457
75 1GZF NIR 13.2701
76 3OTH CLJ 23.0583
77 3OTH TYD 23.0583
78 2VCH UDP 47.1366
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