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 (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 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 = 638.1 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 6XCF - UZP C16 H22 Cl2 N2 O3 CCCCCNC(=O....
8 6XCE - UZM C14 H18 Cl2 N2 O3 S c1cc(c(cc1....
9 2IMB - AHL C6 H15 N5 O2 [H]/N=C(N)....
10 5V8P Ki = 10.2 uM 90G C11 H10 Cl N3 O S c1cc(ccc1c....
11 2ILP ic50 = 15 uM GB5 C9 H8 Cl N O2 c1cc(ccc1C....
12 3DS9 - 01W ARG TRP THR DAB MET LEU GLY n/a n/a
13 5V8R - 90J C11 H10 F N3 O S c1cc(ccc1c....
14 3C8B Ki = 786 nM ARG ARG GLY ILE NH2 n/a n/a
15 3C89 Ki = 845 nM ARG ARG GLY MET NH2 n/a n/a
16 3C8A Ki = 660 nM ARG ARG GLY LEU NH2 n/a n/a
17 3QIY Ki = 4.6 uM QI1 C18 H20 Cl2 N2 O2 c1cc(ccc1C....
18 3C88 Ki = 157 nM ARG ARG GLY CYS NH2 n/a n/a
19 2IMA Ki = 300 nM GB4 C9 H7 Cl2 N O2 c1cc(c(cc1....
20 3BOO Ki = 1.9 uM ACE CSO ARG ALA THR LYS MET LEU n/a n/a
21 4HEV Ki = 460 nM AXM C12 H19 N O2 C1C2CC3CC1....
22 3DDA ic50 = 132.9 uM GLN ARG ALA THR LYS MET NH2 n/a n/a
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 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 = 638.1 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 6XCF - UZP C16 H22 Cl2 N2 O3 CCCCCNC(=O....
8 6XCE - UZM C14 H18 Cl2 N2 O3 S c1cc(c(cc1....
9 2IMB - AHL C6 H15 N5 O2 [H]/N=C(N)....
10 5V8P Ki = 10.2 uM 90G C11 H10 Cl N3 O S c1cc(ccc1c....
11 2ILP ic50 = 15 uM GB5 C9 H8 Cl N O2 c1cc(ccc1C....
12 3DS9 - 01W ARG TRP THR DAB MET LEU GLY n/a n/a
13 5V8R - 90J C11 H10 F N3 O S c1cc(ccc1c....
14 3C8B Ki = 786 nM ARG ARG GLY ILE NH2 n/a n/a
15 3C89 Ki = 845 nM ARG ARG GLY MET NH2 n/a n/a
16 3C8A Ki = 660 nM ARG ARG GLY LEU NH2 n/a n/a
17 3QIY Ki = 4.6 uM QI1 C18 H20 Cl2 N2 O2 c1cc(ccc1C....
18 3C88 Ki = 157 nM ARG ARG GLY CYS NH2 n/a n/a
19 2IMA Ki = 300 nM GB4 C9 H7 Cl2 N O2 c1cc(c(cc1....
20 3BOO Ki = 1.9 uM ACE CSO ARG ALA THR LYS MET LEU n/a n/a
21 4HEV Ki = 460 nM AXM C12 H19 N O2 C1C2CC3CC1....
22 3DDA ic50 = 132.9 uM GLN ARG ALA THR LYS MET NH2 n/a n/a
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 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 = 638.1 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 6XCF - UZP C16 H22 Cl2 N2 O3 CCCCCNC(=O....
8 6XCE - UZM C14 H18 Cl2 N2 O3 S c1cc(c(cc1....
9 2IMB - AHL C6 H15 N5 O2 [H]/N=C(N)....
10 5V8P Ki = 10.2 uM 90G C11 H10 Cl N3 O S c1cc(ccc1c....
11 2ILP ic50 = 15 uM GB5 C9 H8 Cl N O2 c1cc(ccc1C....
12 3DS9 - 01W ARG TRP THR DAB MET LEU GLY n/a n/a
13 5V8R - 90J C11 H10 F N3 O S c1cc(ccc1c....
14 3C8B Ki = 786 nM ARG ARG GLY ILE NH2 n/a n/a
15 3C89 Ki = 845 nM ARG ARG GLY MET NH2 n/a n/a
16 3C8A Ki = 660 nM ARG ARG GLY LEU NH2 n/a n/a
17 3QIY Ki = 4.6 uM QI1 C18 H20 Cl2 N2 O2 c1cc(ccc1C....
18 3C88 Ki = 157 nM ARG ARG GLY CYS NH2 n/a n/a
19 2IMA Ki = 300 nM GB4 C9 H7 Cl2 N O2 c1cc(c(cc1....
20 3BOO Ki = 1.9 uM ACE CSO ARG ALA THR LYS MET LEU n/a n/a
21 4HEV Ki = 460 nM AXM C12 H19 N O2 C1C2CC3CC1....
22 3DDA ic50 = 132.9 uM GLN ARG ALA THR LYS MET NH2 n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ARG ARG ALA THR LYS MET NH2; Similar ligands found: 89
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 0.882979 0.963636
3 ACE CSO ARG ALA THR LYS MET LEU 0.622807 0.84375
4 ARG ARG GLY MET NH2 0.536082 0.821429
5 MET ABA LEU ARG MET THR ALA VAL MET 0.533333 0.912281
6 ALA ARG THR LYS GLN THR ALA ARG LYS 0.526316 0.890909
7 ARG ARG ALA ALA 0.521277 0.763636
8 MET CYS LEU ARG MET THR ALA VAL MET 0.508065 0.946429
9 ARG ILE MET GLU NH2 0.504673 0.807018
10 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.504132 0.84127
11 ALA ARG THR LYS GLN THR ALA ARG 0.5 0.872727
12 MET CYS LEU ARG NLE THR ALA VAL MET 0.496063 0.929825
13 ALA ARG THR M3L GLN THR ALA ARG LYS 0.495495 0.868852
14 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.494949 0.777778
15 LYS ARG LYS 0.494737 0.745455
16 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.485714 0.87037
17 ASN ARG LEU MET LEU THR GLY 0.478261 0.896552
18 ALA ALA LEU THR ARG ALA 0.477064 0.854545
19 GLU ARG GLY MET THR 0.473214 0.859649
20 ACE ALA ARG THR LYS GLN 0.46789 0.888889
21 ALA ARG THR M3L GLN THR ALA ARG 0.466102 0.84127
22 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.466102 0.859649
23 GLU ALA GLN THR ARG LEU 0.453782 0.824561
24 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.45 0.810345
25 MET ALA ARG 0.45 0.836364
26 ILE LEU ASN ALA MET ILE THR LYS ILE 0.448 0.79661
27 ALA ARG 9AT 0.446809 0.851852
28 ALA THR PRK ALA ALA ARG LYS SER 0.446429 0.724138
29 LEU GLU LYS ALA ARG GLY SER THR TYR 0.444444 0.769231
30 GLN ILE LYS VAL ARG VAL ASP MET VAL 0.44186 0.844828
31 ARG GLU ALA ALA 0.441176 0.732143
32 GLN THR ALA ARG M3L SER 0.439024 0.84127
33 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.438776 0.745455
34 THR ILE MET MET GLN ARG GLY 0.436975 0.896552
35 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.435484 0.946429
36 GLU LEU ARG ARG LYS MET MET TYR MET 0.435115 0.809524
37 LYS ALA ALA ARG M3L SER ALA 0.433333 0.83871
38 ALA MET ARG VAL 0.432692 0.818182
39 ALA ARG TPO LYS 0.432432 0.758065
40 SER LEU LYS LEU MET THR THR VAL 0.429825 0.824561
41 MET CYS PRO ARG MET THR ALA VAL MET 0.429577 0.794118
42 GLU LEU LYS ARG LYS MET ILE TYR MET 0.428571 0.78125
43 ASN ARG LEU LEU LEU THR GLY 0.428571 0.827586
44 ALA THR ALY ALA ALA ARG ALY SER ALA PRO 0.428571 0.735294
45 LYS THR LYS LEU LEU 0.428571 0.767857
46 ALA ARG THR ALY GLN THR ALA 0.42735 0.892857
47 LYS MET ASN THR GLN PHE THR ALA VAL 0.426471 0.786885
48 GLN THR ALA ARG M3L SER THR GLY 0.426357 0.84127
49 ALA ARG THR MLY GLN 0.426087 0.852459
50 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.423423 0.821429
51 LYS MET LYS 0.42268 0.745455
52 ALA ARG LYS LEU ASP 0.422018 0.789474
53 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.421875 0.807018
54 ARG ARG GLY LEU NH2 0.421569 0.736842
55 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.421488 0.912281
56 ACE GLU ALA GLN THR ARG LEU 0.421488 0.810345
57 ARG ARG LEU ILE PHE NH2 0.420168 0.711864
58 GLN ARG SER THR SEP THR 0.418033 0.734375
59 ARG ARG GLY ILE NH2 0.417476 0.736842
60 GLU ALA THR GLN LEU MET ASN 0.416667 0.754386
61 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.415493 0.854839
62 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.415254 0.854839
63 ARG ARG PHE AIB ALA MET LEU ALA 0.414815 0.816667
64 ARG ASP ARG ALA ALA LYS LEU 0.414414 0.785714
65 LYS SER ALA TPO THR THR VAL MET ASN PRO 0.413793 0.68254
66 ARG ARG ARG GLU THR GLN VAL 0.412281 0.842105
67 LYS ARG ARG LYS SEP VAL 0.412281 0.71875
68 ARG ARG ARG VAL ARG 00S 0.412281 0.7
69 ALA MET ALA PRO ARG THR LEU LEU LEU 0.411765 0.768116
70 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.411765 0.854839
71 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.410256 0.866667
72 ALA ARG LYS SEP THR GLY GLY LYS 0.409091 0.765625
73 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.408333 0.883333
74 THR ARG SER GLY ALY VAL MET ARG ARG LEU 0.408 0.827586
75 01W ARG TRP THR DAB MET LEU GLY 0.407643 0.646341
76 LEU LYS THR LYS LEU LEU 0.407407 0.767857
77 HIS MET THR GLU VAL VAL ARG ARG CYS 0.407143 0.80303
78 ALA LYS ALA ILE ALA 0.40566 0.654545
79 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.404959 0.928571
80 ALA ARG THR MLY GLN THR ALA ARG LYS 0.404959 0.866667
81 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.40458 0.721311
82 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.404412 0.84127
83 PHE TYR ARG ALA LEU MET 0.402985 0.75
84 THR SER ARG HIS LYS ALY LEU MET ALA 0.402778 0.80597
85 GLU LEU ASN ARG LYS MET ILE TYR MET 0.402685 0.8
86 LYS THR LYS 0.402062 0.745455
87 ARG ARG GLY CYS NH2 0.401961 0.732143
88 HIS MET THR GLU VAL VAL ARG HIS CYS 0.4 0.791045
89 ARG HIS LYS ALY LEU MET PHE LYS 0.4 0.701493
Similar Ligands (3D)
Ligand no: 1; Ligand: ARG ARG ALA THR LYS MET NH2; Similar ligands found: 0
No: Ligand Similarity coefficient
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 with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3c88.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
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