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: 103
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 ARG ASP ARG ALA ALA LYS LEU 0.5 0.785714
13 MET CYS LEU ARG NLE THR ALA VAL MET 0.496063 0.929825
14 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.494949 0.777778
15 LYS ARG LYS 0.494737 0.745455
16 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.49 0.759259
17 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.485714 0.87037
18 PRO PRO LYS LYS LYS ARG LYS VAL 0.485149 0.763636
19 ASN ARG LEU MET LEU THR GLY 0.478261 0.896552
20 ALA ALA LEU THR ARG ALA 0.477064 0.854545
21 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.474576 0.868852
22 GLU ARG GLY MET THR 0.473214 0.859649
23 MET ARG THR GLY ASN ALA XSN 0.471545 0.881356
24 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.471154 0.763636
25 ACE ALA ARG THR LYS GLN 0.46789 0.888889
26 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.466102 0.859649
27 ALA ARG THR M3L GLN THR ALA ARG 0.466102 0.84127
28 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.457627 0.912281
29 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.454545 0.810345
30 GLU ALA GLN THR ARG LEU 0.453782 0.824561
31 ARG ARG PHE AIB ALA MET LEU ALA 0.450382 0.816667
32 MET ALA ARG 0.45 0.836364
33 ALA ARG 9AT 0.446809 0.851852
34 ALA THR PRK ALA ALA ARG LYS SER 0.446429 0.724138
35 LEU GLU LYS ALA ARG GLY SER THR TYR 0.444444 0.769231
36 GLN ILE LYS VAL ARG VAL ASP MET VAL 0.44186 0.844828
37 ARG GLU ALA ALA 0.441176 0.732143
38 GLN THR ALA ARG M3L SER 0.439024 0.84127
39 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.438776 0.745455
40 ALA PRO ALA LEU ARG VAL VAL LYS 0.4375 0.785714
41 THR ILE MET MET GLN ARG GLY 0.436975 0.896552
42 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.435484 0.946429
43 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.435115 0.854839
44 GLU LEU ARG ARG LYS MET MET TYR MET 0.435115 0.809524
45 LYS ALA ALA ARG M3L SER ALA 0.433333 0.83871
46 ALA MET ARG VAL 0.432692 0.818182
47 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.432432 0.862069
48 SER LEU LYS LEU MET THR THR VAL 0.429825 0.824561
49 MET CYS PRO ARG MET THR ALA VAL MET 0.429577 0.794118
50 GLU LEU LYS ARG LYS MET ILE TYR MET 0.428571 0.78125
51 LYS THR LYS LEU LEU 0.428571 0.767857
52 ALA THR ALY ALA ALA ARG ALY SER ALA PRO 0.428571 0.735294
53 ALA ARG THR ALY GLN THR ALA 0.42735 0.892857
54 LYS MET ASN THR GLN PHE THR ALA VAL 0.426471 0.786885
55 GLN THR ALA ARG M3L SER THR GLY 0.426357 0.84127
56 ALA ARG THR MLY GLN 0.426087 0.852459
57 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.423423 0.821429
58 LYS MET LYS 0.42268 0.745455
59 ALA ARG LYS LEU ASP 0.422018 0.789474
60 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.421875 0.807018
61 LYS ALA ARG VAL LEU ALA GLU ALA MET 0.421875 0.807018
62 ARG ARG GLY LEU NH2 0.421569 0.736842
63 ACE GLU ALA GLN THR ARG LEU 0.421488 0.810345
64 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.420561 0.836364
65 ARG ARG LEU ILE PHE NH2 0.420168 0.711864
66 ARG ARG GLY ILE NH2 0.417476 0.736842
67 GLU ALA THR GLN LEU MET ASN 0.416667 0.754386
68 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.415493 0.854839
69 ALA ARG THR M3L GLN THR ALA 0.415254 0.854839
70 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.415254 0.854839
71 LYS SER ALA TPO THR THR VAL MET ASN PRO 0.413793 0.68254
72 ARG ARG ARG VAL ARG 00S 0.412281 0.7
73 LYS ARG ARG LYS SEP VAL 0.412281 0.71875
74 ARG ARG ARG GLU THR GLN VAL 0.412281 0.842105
75 ALA ARG THR M3L GLN THR ALA ARG LYS 0.411765 0.854839
76 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.411765 0.854839
77 ALA MET ALA PRO ARG THR LEU LEU LEU 0.411765 0.768116
78 LYS ALA VAL PHE ASN PHE ALA THR MET 0.410448 0.746032
79 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.410448 0.671875
80 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.410256 0.866667
81 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.41 0.740741
82 ARG ARG ARG ARG ARG ARG ARG ARG 0.41 0.740741
83 ALA ARG LYS SEP THR GLY GLY LYS 0.409091 0.765625
84 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.408333 0.883333
85 ALA ARG THR MLY GLN THR ALA 0.408333 0.883333
86 01W ARG TRP THR DAB MET LEU GLY 0.407643 0.646341
87 LEU LYS THR LYS LEU LEU 0.407407 0.767857
88 LYS GLN THR ALA ARG M3L SER THR GLY 0.406504 0.84127
89 ACE ARG LYS VAL ARG MET 5XU 0.40566 0.818182
90 ALA LYS ALA ILE ALA 0.40566 0.654545
91 ALA ARG THR MLY GLN THR ALA ARG LYS 0.404959 0.866667
92 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.404959 0.928571
93 THR ARG SER GLY ALY VAL MET ARG ARG LEU 0.404762 0.827586
94 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.40458 0.721311
95 GLU GLU GLU ASP GLY TPO MET LYS ARG ASN 0.402985 0.8125
96 PHE TYR ARG ALA LEU MET 0.402985 0.75
97 THR SER ARG HIS LYS ALY LEU MET ALA 0.402778 0.80597
98 GLU LEU ASN ARG LYS MET ILE TYR MET 0.402685 0.8
99 LYS THR LYS 0.402062 0.745455
100 ARG ARG GLY CYS NH2 0.401961 0.732143
101 ASN ARG LEU LEU LEU THR GLY 0.4 0.824561
102 ALA ARG THR MLY GLN THR ALA ARG TYR 0.4 0.791045
103 ARG HIS LYS ALY LEU MET PHE LYS 0.4 0.701493
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 46 residues
No: Leader PDB Ligand Sequence Similarity
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