Receptor
PDB id Resolution Class Description Source Keywords
3DDB 1.6 Å EC: 3.4.24.69 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEUROTOXIN SEROTYPE A WITH A SUBSTRATE ANALOG PEPTIDE CLOSTRIDIUM BOTULINUM BOTULINUM NEUROTOXIN TYPE A BOTOX CATALYTIC DOMAIN ENDOPEPTIDASE SYNTAXIN BIO-WARFARE AGENT HYDROLASE METAL-BINDING METALLOPROTEASE PROTEASE SECRETED TRANSMEMBRANE ZINC ENZYME-SUBSTRATE COMPLEX PHARMACEUTICAL
Ref.: SUBSTRATE BINDING MODE AND ITS IMPLICATION ON DRUG DESIGN FOR BOTULINUM NEUROTOXIN A PLOS PATHOG. V. 4 E1000 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG ARG ALA THR LYS MET NH2 B:197;
Valid;
none;
ic50 = 94.9 uM
766.007 n/a S(CCC...
SO4 A:451;
A:452;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
ZN A:450;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3C88 1.6 Å EC: 3.4.24.69 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEURO SEROTYPE A WITH INHIBITORY PEPTIDE RRGC CLOSTRIDIUM BOTULINUM BOTULINUM NEUROTOXIN TYPE A CATALYTIC DOMAIN ENDOPEPTIDASEWARFARE AGENT PROTEASE SECRETED HYDROLASE-HYDROLASE INHICOMPLEX
Ref.: STRUCTURE- AND SUBSTRATE-BASED INHIBITOR DESIGN FOR CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPE A J.BIOL.CHEM. V. 283 18883 2008
Members (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3DDB ic50 = 94.9 uM ARG ARG ALA THR LYS MET NH2 n/a n/a
2 2G7Q - AHL C6 H15 N5 O2 [H]/N=C(N)....
3 5V8U - 90M C12 H12 F N3 O S Cc1c(n[nH]....
4 3QJ0 Ki = 6.3 uM QI3 C17 H16 Cl2 N2 O5 S c1cc(ccc1O....
5 3NF3 Ki = 638 nM ARG ARG PHE AIB ALA MET LEU ALA n/a n/a
6 3QIZ Ki = 6.1 uM QI2 C24 H32 F2 N2 O3 Cc1cc(ccc1....
7 2IMB - AHL C6 H15 N5 O2 [H]/N=C(N)....
8 5V8P Ki = 10.2 uM 90G C11 H10 Cl N3 O S c1cc(ccc1c....
9 2ILP ic50 = 15 uM GB5 C9 H8 Cl N O2 c1cc(ccc1C....
10 3DS9 - 01W ARG TRP THR DAB MET LEU GLY n/a n/a
11 5V8R - 90J C11 H10 F N3 O S c1cc(ccc1c....
12 3C8B Ki = 786 nM ARG ARG GLY ILE NH2 n/a n/a
13 3C89 Ki = 845 nM ARG ARG GLY MET NH2 n/a n/a
14 3C8A Ki = 660 nM ARG ARG GLY LEU NH2 n/a n/a
15 3QIY Ki = 4.6 uM QI1 C18 H20 Cl2 N2 O2 c1cc(ccc1C....
16 3C88 Ki = 157 nM ARG ARG GLY CYS NH2 n/a n/a
17 2IMA Ki = 300 nM GB4 C9 H7 Cl2 N O2 c1cc(c(cc1....
18 3BOO Ki = 1.9 uM ACE CSO ARG ALA THR LYS MET LEU n/a n/a
19 4HEV Ki = 460 nM AXM C12 H19 N O2 C1C2CC3CC1....
20 3DDA ic50 = 132.9 uM GLN ARG ALA THR LYS MET NH2 n/a n/a
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3DDB ic50 = 94.9 uM ARG ARG ALA THR LYS MET NH2 n/a n/a
2 2G7Q - AHL C6 H15 N5 O2 [H]/N=C(N)....
3 5V8U - 90M C12 H12 F N3 O S Cc1c(n[nH]....
4 3QJ0 Ki = 6.3 uM QI3 C17 H16 Cl2 N2 O5 S c1cc(ccc1O....
5 3NF3 Ki = 638 nM ARG ARG PHE AIB ALA MET LEU ALA n/a n/a
6 3QIZ Ki = 6.1 uM QI2 C24 H32 F2 N2 O3 Cc1cc(ccc1....
7 2IMB - AHL C6 H15 N5 O2 [H]/N=C(N)....
8 5V8P Ki = 10.2 uM 90G C11 H10 Cl N3 O S c1cc(ccc1c....
9 2ILP ic50 = 15 uM GB5 C9 H8 Cl N O2 c1cc(ccc1C....
10 3DS9 - 01W ARG TRP THR DAB MET LEU GLY n/a n/a
11 5V8R - 90J C11 H10 F N3 O S c1cc(ccc1c....
12 3C8B Ki = 786 nM ARG ARG GLY ILE NH2 n/a n/a
13 3C89 Ki = 845 nM ARG ARG GLY MET NH2 n/a n/a
14 3C8A Ki = 660 nM ARG ARG GLY LEU NH2 n/a n/a
15 3QIY Ki = 4.6 uM QI1 C18 H20 Cl2 N2 O2 c1cc(ccc1C....
16 3C88 Ki = 157 nM ARG ARG GLY CYS NH2 n/a n/a
17 2IMA Ki = 300 nM GB4 C9 H7 Cl2 N O2 c1cc(c(cc1....
18 3BOO Ki = 1.9 uM ACE CSO ARG ALA THR LYS MET LEU n/a n/a
19 4HEV Ki = 460 nM AXM C12 H19 N O2 C1C2CC3CC1....
20 3DDA ic50 = 132.9 uM GLN ARG ALA THR LYS MET NH2 n/a n/a
50% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3DDB ic50 = 94.9 uM ARG ARG ALA THR LYS MET NH2 n/a n/a
2 2G7Q - AHL C6 H15 N5 O2 [H]/N=C(N)....
3 5V8U - 90M C12 H12 F N3 O S Cc1c(n[nH]....
4 3QJ0 Ki = 6.3 uM QI3 C17 H16 Cl2 N2 O5 S c1cc(ccc1O....
5 3NF3 Ki = 638 nM ARG ARG PHE AIB ALA MET LEU ALA n/a n/a
6 3QIZ Ki = 6.1 uM QI2 C24 H32 F2 N2 O3 Cc1cc(ccc1....
7 2IMB - AHL C6 H15 N5 O2 [H]/N=C(N)....
8 5V8P Ki = 10.2 uM 90G C11 H10 Cl N3 O S c1cc(ccc1c....
9 2ILP ic50 = 15 uM GB5 C9 H8 Cl N O2 c1cc(ccc1C....
10 3DS9 - 01W ARG TRP THR DAB MET LEU GLY n/a n/a
11 5V8R - 90J C11 H10 F N3 O S c1cc(ccc1c....
12 3C8B Ki = 786 nM ARG ARG GLY ILE NH2 n/a n/a
13 3C89 Ki = 845 nM ARG ARG GLY MET NH2 n/a n/a
14 3C8A Ki = 660 nM ARG ARG GLY LEU NH2 n/a n/a
15 3QIY Ki = 4.6 uM QI1 C18 H20 Cl2 N2 O2 c1cc(ccc1C....
16 3C88 Ki = 157 nM ARG ARG GLY CYS NH2 n/a n/a
17 2IMA Ki = 300 nM GB4 C9 H7 Cl2 N O2 c1cc(c(cc1....
18 3BOO Ki = 1.9 uM ACE CSO ARG ALA THR LYS MET LEU n/a n/a
19 4HEV Ki = 460 nM AXM C12 H19 N O2 C1C2CC3CC1....
20 3DDA ic50 = 132.9 uM GLN ARG ALA THR LYS MET NH2 n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG ARG ALA THR LYS MET NH2; Similar ligands found: 95
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG ARG ALA THR LYS MET NH2 1 1
2 GLN ARG ALA THR LYS MET NH2 0.876405 0.963636
3 ACE CSO ARG ALA THR LYS MET LEU 0.630631 0.84375
4 ARG ARG ALA ALA 0.539326 0.763636
5 ARG ARG GLY MET NH2 0.536842 0.821429
6 MET ABA LEU ARG MET THR ALA VAL MET 0.530435 0.912281
7 MET CYS LEU ARG MET THR ALA VAL MET 0.516949 0.946429
8 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.509091 0.890909
9 ARG ASP ARG ALA ALA LYS LEU 0.50505 0.785714
10 ALA ARG THR LYS GLN THR ALA ARG 0.504505 0.890909
11 ALA ARG THR LYS GLN THR ALA ARG LYS 0.504505 0.890909
12 MET CYS LEU ARG NLE THR ALA VAL MET 0.5 0.929825
13 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.495935 0.854839
14 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.494505 0.763636
15 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.491071 0.859649
16 ASN ARG LEU MET LEU THR GLY 0.491071 0.896552
17 LYS ARG LYS 0.488889 0.745455
18 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.487179 0.929825
19 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.478992 0.84127
20 ARG ARG ARG GLU THR GLN VAL 0.471154 0.807018
21 ALA ARG LYS LEU ASP 0.47 0.789474
22 GLU ALA GLN THR ARG LEU 0.469027 0.824561
23 ARG GLU ALA ALA 0.46875 0.732143
24 LYS ARG LYS ARG LYS ARG LYS ARG 0.46875 0.759259
25 ALA ALA LEU THR ARG ALA 0.46729 0.854545
26 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.464646 0.763636
27 ARG ARG PHE AIB ALA MET LEU ALA 0.460317 0.816667
28 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.456897 0.810345
29 LYS THR LYS LEU LEU 0.454545 0.732143
30 ACE ALA ARG THR LYS GLN 0.45283 0.888889
31 MET ALA ARG 0.452632 0.836364
32 GLU ARG GLY MET THR 0.45045 0.859649
33 GLU ALA THR GLN LEU MET ASN 0.447368 0.754386
34 LEU GLU LYS ALA ARG GLY SER THR TYR 0.446043 0.769231
35 01W ARG TRP THR DAB MET LEU GLY 0.445946 0.646341
36 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.444444 0.912281
37 ALA ARG THR M3L GLN THR ALA ARG 0.444444 0.84127
38 SER LEU LYS LEU MET THR THR VAL 0.444444 0.807018
39 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.444444 0.745455
40 GLN THR ALA ARG M3L SER THR GLY 0.443548 0.84127
41 LYS MET ASN THR GLN PHE THR ALA VAL 0.438462 0.770492
42 GLU LEU ARG ARG LYS MET MET TYR MET 0.435484 0.809524
43 LYS MET LYS 0.434783 0.709091
44 ALA ARG THR MLY GLN THR ALA ARG LYS 0.433333 0.883333
45 ARG ARG ARG TRP ARG ARG LEU THR VAL 0.433071 0.731343
46 ALA THR PRK ALA ALA ARG LYS SER 0.431193 0.706897
47 LYS ALA ALA ARG M3L SER ALA 0.431034 0.83871
48 LYS ALA VAL PHE ASN PHE ALA THR MET 0.429688 0.730159
49 ARG ARG GLY LEU NH2 0.425743 0.736842
50 GLU LEU LYS ARG LYS MET ILE TYR MET 0.425373 0.78125
51 ALA ARG THR MLY GLN 0.423423 0.852459
52 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.423077 0.854839
53 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.422764 0.807018
54 LYS ALA ARG VAL LEU ALA GLU ALA MET 0.422764 0.807018
55 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.422018 0.862069
56 ARG ARG ARG ARG ARG ARG ARG ARG 0.421053 0.740741
57 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.421053 0.745455
58 ARG ARG LEU ILE PHE NH2 0.418803 0.711864
59 ACE ALA ARG THR GLU VAL TYR NH2 0.418033 0.730159
60 LYS ALA VAL TYR ASN LEU ALA THR MET 0.41791 0.71875
61 LEU LYS THR LYS LEU LEU 0.417476 0.732143
62 ALA ARG THR ALY GLN THR ALA 0.417391 0.892857
63 LYS GLN THR ALA ARG M3L SER THR GLY 0.416667 0.84127
64 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.415929 0.866667
65 SER ARG TYR TRP ALA ILE ARG THR ARG 0.413793 0.690141
66 LYS THR LYS 0.413043 0.709091
67 ALA MET ARG VAL 0.411765 0.818182
68 LYS ALA LEU TYR ASN PHE ALA THR MET 0.411765 0.69697
69 ARG ARG GLY ILE NH2 0.411765 0.736842
70 LYS LYS LYS ALA 0.411111 0.618182
71 PHE TYR ARG ALA LEU MET 0.410853 0.75
72 LYS SER ALA TPO THR THR VAL MET ASN PRO 0.410714 0.666667
73 ACE ALC ARG ALA MET CY1 SER LEU NH2 0.410448 0.822581
74 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.410256 0.928571
75 ACE ARG LYS VAL ARG MET 5XU 0.407767 0.818182
76 LYS ALA VAL TYR ASN PHE ALA THR MET 0.407407 0.69697
77 GLN ARG SER THR SEP THR 0.40678 0.734375
78 THR PRO THR ARG ASP VAL ALA THR SER PRO 0.40625 0.685714
79 ALA MET ALA PRO ARG THR LEU LEU LEU 0.406015 0.768116
80 LEU PRO PHE GLU ARG ALA THR VAL MET 0.405229 0.746479
81 ALA ARG THR MLY GLN THR ALA ARG TYR 0.40458 0.791045
82 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.40367 0.821429
83 THR ILE MET MET GLN ARG GLY 0.403361 0.896552
84 THR SER ARG HIS LYS ALY LEU MET ALA 0.402878 0.80597
85 ALA ARG THR M3L GLN THR ALA 0.401709 0.854839
86 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.401709 0.854839
87 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.401709 0.883333
88 ALA ARG THR MLY GLN THR ALA 0.401709 0.883333
89 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.401709 0.854839
90 THR ARG SER GLY ALY VAL MET ARG ARG LEU 0.401639 0.827586
91 ACE GLN THR ALA ARG KCR SER THR 0.4 0.844828
92 VAL ALA ARG SER 0.4 0.754386
93 ALA GLN THR ALA ARG ALY SER THR 0.4 0.877193
94 ARG ALA ARG 0.4 0.722222
95 THR ARG ARG GLU THR GLN LEU 0.4 0.859649
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3C88; Ligand: ARG ARG GLY CYS NH2; Similar sites found: 22
This union binding pocket(no: 1) in the query (biounit: 3c88.bio1) has 46 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4OAS 2SW 0.0202 0.41913 2.08333
2 2NPA MMB 0.02132 0.40293 2.22222
3 5AMC GLY NIY 0.005989 0.45903 2.31481
4 1TMX HGX 0.01113 0.41592 2.38908
5 4ISS TAR 0.04968 0.41317 2.63975
6 5KDX GAL TNR 0.01749 0.4397 3.24074
7 3FW3 GLC 0.00993 0.40449 3.38346
8 2OKL BB2 0.03022 0.40407 3.78378
9 3G5K BB2 0.02603 0.4103 3.82514
10 4UCC ZKW 0.03853 0.40234 3.86266
11 2JHP GUN 0.001929 0.47453 4.39815
12 3B6C SDN 0.02387 0.43059 4.70085
13 4LWU 20U 0.01266 0.42945 4.70588
14 1MMQ RRS 0.00618 0.43767 7.05882
15 1G27 BB1 0.01003 0.42416 7.14286
16 1R55 097 0.02923 0.42162 7.47664
17 5JF2 SF7 0.02016 0.40966 7.84314
18 2ZWS PLM 0.01047 0.4462 9.9537
19 5OCA 9QZ 0.02297 0.43049 10.5042
20 1M2Z BOG 0.01434 0.44367 10.8949
21 1WS1 BB2 0.01017 0.43062 11.5385
22 3D3X ARG ILE MET GLU NH2 0.0000009017 0.59668 49.6487
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