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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 62 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 (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 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 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: 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 : 2VL8; Ligand: CTS; Similar sites found with APoc: 94
This union binding pocket(no: 1) in the query (biounit: 2vl8.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1ZED PNP 1.23967
3 5ZKC 3C0 1.42518
4 5CX8 TG6 1.6632
5 2J0B UDP 1.78571
6 3B9Z CO2 1.80412
7 1TSD UMP 1.88679
8 1EWK GLU 2.04082
9 4CLR FDB 2.08333
10 2JC9 ADN 2.1978
11 2UYQ SAM 2.25806
12 3U2U UDP 2.28137
13 4DE3 DN8 2.28137
14 4DDY DN6 2.28137
15 6CS8 F9Y 2.31023
16 2P6W FLC 2.34742
17 6MVU K4V 2.38095
18 4IRP UDP 2.39044
19 4ZGM 32M 2.45902
20 4UP4 GAL NAG 2.49377
21 6CGN DA 2.5641
22 1LL2 UPG 2.7027
23 4P86 5GP 2.73224
24 5NDF LU2 2.9304
25 5NDF UDP 2.9304
26 5FPN KYD 2.9304
27 1I0B PEL 3.01205
28 2WZG UPG 3.04762
29 3V91 UPG 3.09278
30 6F7L FAD 3.16742
31 6H21 UD1 3.18841
32 4RKK GLC GLC GLC GLC GLC GLC 3.31325
33 6EYT UDP 3.36391
34 6EYT NDG 3.36391
35 1JG3 ADN 3.40426
36 1O7Q UDP 3.46021
37 1O7Q GAL NAG 3.46021
38 5E5U MLT 3.51759
39 1LNX URI 3.7037
40 4M37 SAH 3.79009
41 6BSW UDP 3.84615
42 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 4.0153
43 1SAY PYR 4.0293
44 5N5U 7N8 4.14013
45 1PNF NDG NAG 4.14013
46 2WZF UDP 4.19048
47 2WZF BGC 4.19048
48 1QMG DMV 4.19847
49 6BGC BGC 4.39277
50 2QES ADE 4.5977
51 5H62 UDP 4.88506
52 5LX9 OLB 4.92958
53 2WPB ZZI 4.93421
54 3WUR O4B 5.26316
55 1N2X SAM 5.64784
56 2VOH CIT 5.73248
57 1FO3 KIF 5.86957
58 3OG9 MLT 6.2201
59 3CV2 COA 6.39098
60 1MID LAP 6.59341
61 1A78 TDG 6.71642
62 4TVD BGC 6.77656
63 5Z3I ADE 7.16981
64 4I90 CHT 7.92079
65 5MDH MAK 8.10811
66 1GA8 DEL 8.36013
67 1GA8 UPF 8.36013
68 6CB2 OLC 8.53242
69 1YRO GDU 8.74126
70 4OGQ 1O2 8.82353
71 4POO SAM 9
72 3CU0 GAL GAL SO4 9.25267
73 3CU0 UDP 9.25267
74 4IHL 1F5 11.1111
75 3KP6 SAL 11.2583
76 5LWY OLB 11.7647
77 2DM6 NAP 12.012
78 1V84 UDP 12.6482
79 5M36 9SZ 13.1579
80 5V4R MGT 16.6667
81 4DXJ 0M9 16.8508
82 4M4K GDU 17.0732
83 4M4K XYP XYP 17.0732
84 3IOI 1GW 17.1141
85 1NU4 MLA 17.5258
86 5Z84 CHD 20.5479
87 5ZCO CHD 20.5479
88 5W97 CHD 20.5479
89 1V6A TRE 20.7831
90 4MIX UD1 23.8095
91 5M37 9SZ 25
92 3GDH SAH 25.7261
93 5MWE TCE 25.9259
94 2Y69 CHD 27.1429
Pocket No.: 2; Query (leader) PDB : 2VL8; Ligand: UDP; Similar sites found with APoc: 101
This union binding pocket(no: 2) in the query (biounit: 2vl8.bio2) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 5VCM UDP 1.19332
3 1ZED PNP 1.23967
4 5ZKC 3C0 1.42518
5 5CX8 TG6 1.6632
6 2J0B UDP 1.78571
7 3B9Z CO2 1.80412
8 1NCE UMP 1.89394
9 1EWK GLU 2.04082
10 2JC9 ADN 2.1978
11 2UYQ SAM 2.25806
12 3U2U UDP 2.28137
13 4DE3 DN8 2.28137
14 4DDY DN6 2.28137
15 6CS8 F9Y 2.31023
16 2P6W FLC 2.34742
17 2AF6 BRU 2.38095
18 6MVU K4V 2.38095
19 4IRP UDP 2.39044
20 4ZGM 32M 2.45902
21 4UP4 GAL NAG 2.49377
22 6CGN DA 2.5641
23 1LL2 UPG 2.7027
24 5J32 IPM 2.72953
25 4P86 5GP 2.73224
26 5NDF LU2 2.9304
27 5NDF UDP 2.9304
28 5FPN KYD 2.9304
29 1I0B PEL 3.01205
30 2WZG UPG 3.04762
31 3V91 UPG 3.09278
32 6F7L FAD 3.16742
33 6H21 UD1 3.18841
34 4RKK GLC GLC GLC GLC GLC GLC 3.31325
35 6EYT UDP 3.36391
36 6EYT NDG 3.36391
37 1JG3 ADN 3.40426
38 1O7Q UDP 3.46021
39 1O7Q GAL NAG 3.46021
40 5E5U MLT 3.51759
41 1LNX URI 3.7037
42 6BSW UDP 3.84615
43 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 4.0153
44 5N5U 7N8 4.14013
45 1PNF NDG NAG 4.14013
46 2WZF UDP 4.19048
47 2WZF BGC 4.19048
48 1QMG DMV 4.19847
49 6BGC BGC 4.39277
50 1WNB BTL 4.44444
51 4XNV BUR 4.51306
52 2QES ADE 4.5977
53 5H62 UDP 4.88506
54 5LX9 OLB 4.92958
55 2WPB ZZI 4.93421
56 3NFD COA 5.22876
57 3WUR O4B 5.26316
58 2VOH CIT 5.73248
59 1FO3 KIF 5.86957
60 3OYW TDG 5.97015
61 5UC9 MYR 6.19469
62 3OG9 MLT 6.2201
63 3CV2 COA 6.39098
64 1MID LAP 6.59341
65 4TVD BGC 6.77656
66 1XVB BBX 7.05882
67 5Z3I ADE 7.16981
68 4I90 CHT 7.92079
69 5MDH MAK 8.10811
70 1SLT NDG GAL 8.20895
71 1GA8 UPF 8.36013
72 1GA8 DEL 8.36013
73 6CB2 OLC 8.53242
74 1YRO GDU 8.74126
75 4OGQ 1O2 8.82353
76 4POO SAM 9
77 3CU0 GAL GAL SO4 9.25267
78 3CU0 UDP 9.25267
79 4M1U A2G MBG 10
80 3A4T SFG 10.9489
81 4IHL 1F5 11.1111
82 3KP6 SAL 11.2583
83 5LWY OLB 11.7647
84 4OB6 S2T 12.0235
85 3WUD GLC GAL 12.5
86 1V84 UDP 12.6482
87 5M36 9SZ 13.1579
88 5V4R MGT 16.6667
89 4DXJ 0M9 16.8508
90 4M4K GDU 17.0732
91 4M4K XYP XYP 17.0732
92 1NU4 MLA 17.5258
93 2HJ9 AI2 19.457
94 5Z84 CHD 20.5479
95 5ZCO CHD 20.5479
96 5W97 CHD 20.5479
97 1V6A TRE 20.7831
98 4MIX UD1 23.8095
99 5M37 9SZ 25
100 5MWE TCE 25.9259
101 2Y69 CHD 27.1429
Pocket No.: 3; Query (leader) PDB : 2VL8; Ligand: UDP; Similar sites found with APoc: 65
This union binding pocket(no: 3) in the query (biounit: 2vl8.bio3) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 1N1G BCP 1.63934
2 1F0X FAD 1.64835
3 5U97 PIT 1.90114
4 1ZPD CIT 2.01465
5 6BMS POV 2.05279
6 5XQL C2E 2.06186
7 4CLR FDB 2.08333
8 1FX8 BOG 2.13523
9 5O42 9JW 2.18978
10 5O42 BGC 2.18978
11 5O42 NAD 2.18978
12 6HL7 CP 2.29885
13 2O1V ADP 2.38095
14 4IPE ANP 2.38095
15 1H9G COA MYR 2.46914
16 4U0I 0LI 2.53968
17 1GNI OLA 2.74725
18 4G86 BNT 2.8169
19 1TV5 N8E 3.11355
20 3GZ9 D32 3.34572
21 4Q0A 4OA 3.64238
22 5AAV GW5 3.96825
23 4TV1 36M 3.98406
24 3K00 MTT 4.64548
25 1R6N 434 5.21327
26 3IX9 MTX 5.26316
27 4IA6 EIC 5.31136
28 2ZKJ ADP 5.58376
29 2HHP FLC 5.66038
30 3HRD FAD 5.74324
31 5EW9 5VC 5.90406
32 5LXT GTP 6.29371
33 4WGF HX2 6.34146
34 6BR8 6OU 6.74603
35 3B6C SDN 6.83761
36 4V1F BQ1 6.97674
37 2WOR 2AN 7
38 3FAL REA 7.02479
39 1FM9 9CR 7.14286
40 4POJ 2VP 7.35931
41 4M8E 29V 7.35931
42 6A5Y 9CR 7.45614
43 4EKQ NPO 7.48663
44 3G4Q MCH 7.53425
45 3G5D 1N1 7.69231
46 5DEY 59T 7.74411
47 3LN0 52B 8.05861
48 2D5Z L35 8.90411
49 3OKI OKI 9.01288
50 3S6X SIA GAL BGC 9.23077
51 4OAS 2SW 9.375
52 6GNO XDI 9.62963
53 3KMZ EQO 9.77444
54 1DKF BMS 11.0638
55 3KU0 ADE 11.9522
56 6MB9 NMY 13.1387
57 4I67 G G G RPC 13.7931
58 1GPJ CIT 16.0891
59 3KO0 TFP 16.8317
60 3N7S 3N7 18.75
61 5MT9 ARG 19.0476
62 5MT9 SRO 19.0476
63 4ZOH FAD 21.4286
64 4ELG 52J 27.1084
65 4ELG 52I 27.1084
Pocket No.: 4; Query (leader) PDB : 2VL8; Ligand: CTS; Similar sites found with APoc: 59
This union binding pocket(no: 4) in the query (biounit: 2vl8.bio3) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1PTR PRB None
2 1F0X FAD 1.64835
3 2JK0 ASP 1.84615
4 1NCE UMP 1.89394
5 1ZPD CIT 2.01465
6 6BMS POV 2.05279
7 1FX8 BOG 2.13523
8 1USR SIA 2.20264
9 3HVJ 705 2.26244
10 2O1V ADP 2.38095
11 3A3B FMN 2.63158
12 4G86 BNT 2.8169
13 1TV5 N8E 3.11355
14 6G47 SIA 3.34928
15 4M5P 23W 3.4398
16 4Q0A 4OA 3.64238
17 4M38 SAH 3.79009
18 5AAV GW5 3.96825
19 4TV1 36M 3.98406
20 4XCP PLM 4.11765
21 6DIO CIT 4.1958
22 4XNV BUR 4.51306
23 4V3I ASP LEU THR ARG PRO 4.66926
24 1R6N 434 5.21327
25 4IA6 EIC 5.31136
26 3QVP FAD 5.31136
27 1WPQ 13P 5.44413
28 2ZKJ ADP 5.58376
29 2HHP FLC 5.66038
30 5EW9 5VC 5.90406
31 1GPE FAD 6.04396
32 5UC9 MYR 6.19469
33 4WGF HX2 6.34146
34 6BR8 6OU 6.74603
35 4V1F BQ1 6.97674
36 2WOR 2AN 7
37 3FAL REA 7.02479
38 1XVB BBX 7.05882
39 1XVB 3BR 7.05882
40 6A5Y 9CR 7.45614
41 4EKQ NPO 7.48663
42 1QCI ADE 7.63359
43 3G5D 1N1 7.69231
44 3LN0 52B 8.05861
45 2D5Z L35 8.90411
46 3S6X SIA GAL BGC 9.23077
47 4URN NOV 9.33333
48 3KMZ EQO 9.77444
49 5V8E CIT 10.6796
50 3KU0 ADE 11.9522
51 6MB9 NMY 13.1387
52 4I67 G G G RPC 13.7931
53 2WJH GDP 15.0602
54 3QUZ QUV 15.311
55 1GPJ CIT 16.0891
56 4USI AKG 16.8831
57 3N7S 3N7 18.75
58 4ELG 52I 27.1084
59 4ELG 52J 27.1084
Pocket No.: 5; Query (leader) PDB : 2VL8; Ligand: UDP; Similar sites found with APoc: 14
This union binding pocket(no: 5) in the query (biounit: 2vl8.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5AZC PGT 2.33333
2 5OPM DTP 2.51046
3 4G6I RS3 2.85714
4 3KDU NKS 3.2491
5 2BHW XAT 3.44828
6 4XCP PLM 4.11765
7 3DFR MTX 4.32099
8 2H5Z CTO 4.91803
9 4XZ3 ACP 5.21739
10 3AQT RCO 5.71429
11 5LXT GDP 6.29371
12 3TDC 0EU 7.32601
13 2I0G I0G 7.7821
14 1M2Z BOG 33.3333
Pocket No.: 6; Query (leader) PDB : 2VL8; Ligand: CTS; Similar sites found with APoc: 12
This union binding pocket(no: 6) in the query (biounit: 2vl8.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1AIQ UMP 1.89394
2 1ZPR UMP 1.89394
3 4DE2 DN3 2.28137
4 2PWY SAH 3.10078
5 2BHW XAT 3.44828
6 3DFR MTX 4.32099
7 2J9L ATP 4.86486
8 3IX9 MTX 5.26316
9 3AQT RCO 5.71429
10 3TDC 0EU 7.32601
11 3MB5 SAM 7.84314
12 4AVV CD 11.2745
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