Receptor
PDB id Resolution Class Description Source Keywords
2VL8 2.31 Å NON-ENZYME: TOXIN_VIRAL CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF LETHAL TOXIN FROM CLOSTRIDIUM SORDELLII IN COMPLEX WITH UDP, C ASTANOSPERMINE AND CALCIUM ION CLOSTRIDIUM SORDELLII TOXIN GLYCOSYLTRANSFERASE
Ref.: INHIBITION OF THE GLUCOSYLTRANSFERASE ACTIVITY OF CLOSTRIDIAL RHO/RAS-GLUCOSYLATING TOXINS BY CASTANOSPERMINE. FEBS LETT. V. 582 2277 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1545;
A:1546;
A:1547;
B:1545;
C:1545;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
CTS A:1544;
B:1544;
C:1544;
Valid;
Valid;
Valid;
none;
none;
none;
ic50 ~ 30 uM
189.209 C8 H15 N O4 C1C[N...
UDP A:1543;
B:1543;
C:1543;
Valid;
Valid;
Valid;
none;
none;
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
2VL8 2.31 Å NON-ENZYME: TOXIN_VIRAL CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF LETHAL TOXIN FROM CLOSTRIDIUM SORDELLII IN COMPLEX WITH UDP, C ASTANOSPERMINE AND CALCIUM ION CLOSTRIDIUM SORDELLII TOXIN GLYCOSYLTRANSFERASE
Ref.: INHIBITION OF THE GLUCOSYLTRANSFERASE ACTIVITY OF CLOSTRIDIAL RHO/RAS-GLUCOSYLATING TOXINS BY CASTANOSPERMINE. FEBS LETT. V. 582 2277 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 60 families.
1 2VKH - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
2 2VL8 ic50 ~ 30 uM CTS C8 H15 N O4 C1C[N@]2C[....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 5UQM - U2F C15 H23 F N2 O16 P2 C1=CN(C(=O....
2 2BVL - GLC C6 H12 O6 C([C@@H]1[....
3 5UQN - U2F C15 H23 F N2 O16 P2 C1=CN(C(=O....
4 2VKH - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
5 2VL8 ic50 ~ 30 uM CTS C8 H15 N O4 C1C[N@]2C[....
6 4DMW - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
7 5UQL - U2F C15 H23 F N2 O16 P2 C1=CN(C(=O....
8 5UQK - U2F C15 H23 F N2 O16 P2 C1=CN(C(=O....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 5UQM - U2F C15 H23 F N2 O16 P2 C1=CN(C(=O....
2 2BVL - GLC C6 H12 O6 C([C@@H]1[....
3 5UQN - U2F C15 H23 F N2 O16 P2 C1=CN(C(=O....
4 2VKH - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
5 2VL8 ic50 ~ 30 uM CTS C8 H15 N O4 C1C[N@]2C[....
6 4DMW - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
7 5UQL - U2F C15 H23 F N2 O16 P2 C1=CN(C(=O....
8 5UQK - U2F C15 H23 F N2 O16 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CTS; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 CTS 1 1
2 X05 0.55 0.897959
3 SWA 0.487179 0.977778
4 GC2 0.44898 0.814815
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 : 2VL8; Ligand: CTS; Similar sites found: 34
This union binding pocket(no: 1) in the query (biounit: 2vl8.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5CX8 TG6 0.01314 0.41264 1.6632
2 3B9Z CO2 0.01896 0.41474 1.80412
3 2UYQ SAM 0.03044 0.40081 2.25806
4 3U2U UDP 0.0005623 0.46818 2.28137
5 4IRP UDP 0.00736 0.4309 2.39044
6 4ZGM 32M 0.01242 0.42176 2.45902
7 1LL2 UPG 0.002458 0.40759 2.7027
8 5FV9 Y6W 0.001704 0.40437 2.9304
9 5FV9 UDP 0.001704 0.40437 2.9304
10 1I0B PEL 0.02537 0.41161 3.01205
11 3JSZ UPG 0.00000001089 0.62129 3.04762
12 3V91 UPG 0.002401 0.40385 3.09278
13 4M37 SAH 0.003922 0.41291 3.79009
14 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 0.008397 0.41683 4.0153
15 1SAY PYR 0.01122 0.41119 4.0293
16 2WZF BGC 0.000001466 0.62111 4.19048
17 2WZF UDP 0.0000122 0.53773 4.19048
18 1QMG DMV 0.01528 0.41228 4.19847
19 2QES ADE 0.01184 0.4172 4.5977
20 2VOH CIT 0.004291 0.44158 5.73248
21 3OG9 MLT 0.02016 0.40786 6.2201
22 3CV2 COA 0.0202 0.40797 6.39098
23 5H4I 7HQ 0.04984 0.40072 7.30337
24 4I90 CHT 0.01127 0.40716 7.92079
25 1GA8 UPF 0.00009763 0.4368 8.36013
26 3CU0 GAL GAL SO4 0.006235 0.42057 9.25267
27 3CU0 UDP 0.003834 0.4114 9.25267
28 4IHL 1F5 0.01449 0.40407 11.1111
29 5V4R MGT 0.01943 0.41475 16.6667
30 4M4K GDU 0.001487 0.41589 17.0732
31 4M4K XYP XYP 0.001487 0.41589 17.0732
32 3IOI 1GW 0.009686 0.41183 17.1141
33 4MIX UD1 0.000000005765 0.68017 23.8095
34 5MWE TCE 0.01665 0.40959 25.9259
Pocket No.: 2; Query (leader) PDB : 2VL8; Ligand: UDP; Similar sites found: 38
This union binding pocket(no: 2) in the query (biounit: 2vl8.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5CX8 TG6 0.01411 0.41264 1.6632
2 3B9Z CO2 0.02022 0.41474 1.80412
3 2UYQ SAM 0.03269 0.40081 2.25806
4 3U2U UDP 0.0005085 0.46586 2.28137
5 2AF6 BRU 0.01649 0.41214 2.38095
6 4IRP UDP 0.01097 0.42265 2.39044
7 4ZGM 32M 0.01334 0.42176 2.45902
8 1LL2 UPG 0.002644 0.41078 2.7027
9 5J32 IPM 0.01523 0.41569 2.72953
10 5FV9 Y6W 0.002223 0.40343 2.9304
11 5FV9 UDP 0.002223 0.40343 2.9304
12 1I0B PEL 0.02708 0.41161 3.01205
13 3JSZ UPG 0.00000001914 0.62049 3.04762
14 3V91 UPG 0.002165 0.40921 3.09278
15 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 0.009015 0.41683 4.0153
16 2WZF BGC 0.000001661 0.62111 4.19048
17 2WZF UDP 0.00001197 0.54072 4.19048
18 1WNB BTL 0.01051 0.40463 4.44444
19 4XNV BUR 0.02182 0.41041 4.51306
20 2QES ADE 0.01275 0.4172 4.5977
21 2VOH CIT 0.003111 0.4477 5.73248
22 5UC9 MYR 0.02756 0.40281 6.19469
23 3OG9 MLT 0.0217 0.40786 6.2201
24 3CV2 COA 0.02169 0.40797 6.39098
25 1XVB BBX 0.006294 0.40876 7.05882
26 4I90 CHT 0.01214 0.40716 7.92079
27 1GA8 UPF 0.0001211 0.43995 8.36013
28 1GA8 DEL 0.0002037 0.40257 8.36013
29 3CU0 GAL GAL SO4 0.008295 0.41169 9.25267
30 3CU0 UDP 0.003911 0.40521 9.25267
31 3A4T SFG 0.003623 0.40025 10.9489
32 4IHL 1F5 0.01891 0.4002 11.1111
33 5V4R MGT 0.02082 0.41475 16.6667
34 4M4K XYP XYP 0.00165 0.41894 17.0732
35 4M4K GDU 0.00165 0.41894 17.0732
36 3IOI 1GW 0.009898 0.40825 17.1141
37 4MIX UD1 0.000000006891 0.68017 23.8095
38 5MWE TCE 0.01367 0.41575 25.9259
Pocket No.: 3; Query (leader) PDB : 2VL8; Ligand: UDP; Similar sites found: 22
This union binding pocket(no: 3) in the query (biounit: 2vl8.bio3) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CLR FDB 0.02508 0.40337 2.08333
2 1H9G COA MYR 0.01301 0.40282 2.46914
3 4U0I 0LI 0.01745 0.40082 2.53968
4 1TV5 N8E 0.02885 0.40324 3.11355
5 1LNX URI 0.003093 0.44762 3.7037
6 1XIU REA 0.004446 0.41026 3.91304
7 1R6N 434 0.01891 0.40619 5.21327
8 3IX9 MTX 0.01103 0.40386 5.26316
9 2ZKJ ADP 0.02132 0.40534 5.58376
10 2HHP FLC 0.00006429 0.49695 5.66038
11 3HRD FAD 0.0259 0.404 5.74324
12 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.03025 0.40026 5.78231
13 4WGF HX2 0.02403 0.40474 6.34146
14 3B6C SDN 0.02099 0.40262 6.83761
15 3FAL REA 0.009192 0.40367 7.02479
16 1FM9 9CR 0.006304 0.40748 7.14286
17 5H4I 7HQ 0.04453 0.40055 7.30337
18 4POJ 2VP 0.00614 0.41315 7.35931
19 3S6X SIA GAL BGC 0.01908 0.40345 9.23077
20 3KU0 ADE 0.0147 0.41013 11.9522
21 4I67 G G G RPC 0.002462 0.43919 13.7931
22 3N7S 3N7 0.02304 0.40285 18.75
Pocket No.: 4; Query (leader) PDB : 2VL8; Ligand: CTS; Similar sites found: 24
This union binding pocket(no: 4) in the query (biounit: 2vl8.bio3) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PTR PRB 0.01812 0.41027 None
2 3HVJ 705 0.002207 0.44346 2.26244
3 3A3B FMN 0.01612 0.40768 2.63158
4 1TV5 N8E 0.03324 0.40324 3.11355
5 4M5P 23W 0.02633 0.40002 3.4398
6 1LNX URI 0.003688 0.44762 3.7037
7 1XIU REA 0.00486 0.41248 3.91304
8 4TV1 36M 0.01267 0.41745 3.98406
9 4XNV BUR 0.01707 0.4172 4.51306
10 4V3I ASP LEU THR ARG PRO 0.02194 0.40835 4.66926
11 1R6N 434 0.01824 0.41115 5.21327
12 2ZKJ ADP 0.0153 0.40613 5.58376
13 2HHP FLC 0.00007611 0.49695 5.66038
14 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.03467 0.40026 5.78231
15 5UC9 MYR 0.02082 0.40924 6.19469
16 4WGF HX2 0.01939 0.41185 6.34146
17 3FAL REA 0.01108 0.40367 7.02479
18 1XVB BBX 0.003662 0.42048 7.05882
19 1GA8 DEL 0.0001872 0.40099 8.36013
20 3S6X SIA GAL BGC 0.0221 0.40345 9.23077
21 4URN NOV 0.0115 0.41961 9.33333
22 3KU0 ADE 0.01707 0.41013 11.9522
23 4I67 G G G RPC 0.01356 0.40725 13.7931
24 3N7S 3N7 0.02242 0.40628 18.75
Pocket No.: 5; Query (leader) PDB : 2VL8; Ligand: UDP; Similar sites found: 7
This union binding pocket(no: 5) in the query (biounit: 2vl8.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4UP4 GAL NAG 0.0237 0.40228 2.49377
2 3KDU NKS 0.02501 0.40597 3.2491
3 3DFR MTX 0.01343 0.40171 4.32099
4 3AQT RCO 0.02977 0.40069 5.71429
5 3TDC 0EU 0.01958 0.4283 7.32601
6 2I0G I0G 0.03503 0.40041 7.7821
7 4ELG 52J 0.002197 0.40291 27.1084
Pocket No.: 6; Query (leader) PDB : 2VL8; Ligand: CTS; Similar sites found: 7
This union binding pocket(no: 6) in the query (biounit: 2vl8.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4UP4 GAL NAG 0.02706 0.40228 2.49377
2 2PWY SAH 0.005313 0.40578 3.10078
3 3DFR MTX 0.01612 0.40142 4.32099
4 3IX9 MTX 0.01279 0.40623 5.26316
5 3AQT RCO 0.03331 0.40124 5.71429
6 3TDC 0EU 0.02196 0.4283 7.32601
7 4ELG 52J 0.003849 0.40239 27.1084
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