Receptor
PDB id Resolution Class Description Source Keywords
3DDA 1.5 Å EC: 3.4.24.69 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEUROTOXIN SEROTYPE A WITH A SNAP-25 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 ALTERNATIVE SPLICING CELL JUNCTION COILEDCOIL LIPOPROTEIN PALMITATE PHOSPHOPROTEIN SYNAPSE SYNAPTOSOME
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
GLN ARG ALA THR LYS MET NH2 B:197;
 Valid;
 none;
 ic50 = 132.9 uM
736.941 n/a S(CCC...
SO4 A:451;
 Invalid;
 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: GLN ARG ALA THR LYS MET NH2; Similar ligands found: 70
No: Ligand ECFP6 Tc MDL keys Tc
1 GLN ARG ALA THR LYS MET NH2 1 1
2 ARG ARG ALA THR LYS MET NH2 0.882979 0.963636
3 ACE CSO ARG ALA THR LYS MET LEU 0.583333 0.84375
4 ALA ARG THR LYS GLN THR ALA ARG LYS 0.543103 0.890909
5 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.520325 0.84127
6 ALA ARG THR LYS GLN THR ALA ARG 0.518182 0.907407
7 GLN THR ALA ARG M3L SER 0.516667 0.84127
8 GLN ILE LYS VAL ARG VAL ASP MET VAL 0.515873 0.877193
9 MET ABA LEU ARG MET THR ALA VAL MET 0.512 0.912281
10 GLU ALA GLN THR ARG LEU 0.508475 0.857143
11 GLN THR ALA ARG M3L SER THR GLY 0.5 0.84127
12 GLN ARG SER THR SEP THR 0.495798 0.734375
13 GLU ARG GLY MET THR 0.491228 0.892857
14 MET CYS LEU ARG MET THR ALA VAL MET 0.488372 0.912281
15 ALA ARG THR M3L GLN THR ALA ARG 0.483333 0.84127
16 MET CYS LEU ARG NLE THR ALA VAL MET 0.477273 0.896552
17 GLU ALA THR GLN LEU MET ASN 0.470588 0.785714
18 ASN ARG LEU MET LEU THR GLY 0.470588 0.896552
19 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.467213 0.842105
20 ARG ARG GLY MET NH2 0.466667 0.821429
21 THR ILE MET MET GLN ARG GLY 0.466667 0.929825
22 ALA ARG THR M3L GLN THR ALA ARG LYS 0.461538 0.83871
23 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.459016 0.859649
24 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.457143 0.745455
25 ARG ILE MET GLU NH2 0.45614 0.839286
26 LYS ARG LYS 0.455446 0.745455
27 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.452381 0.946429
28 GLU LEU ARG ARG LYS MET MET TYR MET 0.451128 0.809524
29 ARG ARG ALA ALA 0.45098 0.732143
30 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.45082 0.946429
31 ACE GLU ALA GLN THR ARG LEU 0.45082 0.842105
32 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.45045 0.836364
33 ACE ALA ARG THR LYS GLN 0.447368 0.888889
34 ALA ARG THR ALY GLN THR ALA 0.445378 0.892857
35 ALA ARG THR MLY GLN 0.444444 0.883333
36 GLU LEU LYS ARG LYS MET ILE TYR MET 0.443662 0.809524
37 ALA ALA LEU THR ARG ALA 0.443478 0.854545
38 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.442478 0.854545
39 LYS MET ASN THR GLN PHE THR ALA VAL 0.442029 0.786885
40 ILE LEU ASN ALA MET ILE THR LYS ILE 0.44186 0.79661
41 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.440559 0.854839
42 LEU GLU LYS ALA ARG GLY SER THR TYR 0.439189 0.769231
43 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.433333 0.854839
44 ARG ARG ARG GLU THR GLN VAL 0.431034 0.842105
45 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.430657 0.84127
46 GLN VAL PRO LEU ARG PRO MET THR TYR LYS 0.430303 0.72973
47 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.429752 0.854839
48 MET ALA ARG 0.428571 0.836364
49 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.428571 0.898305
50 GLU LEU ASN ARG LYS MET ILE TYR MET 0.426667 0.828125
51 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.42623 0.883333
52 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.422764 0.963636
53 ALA ARG THR MLY GLN THR ALA ARG LYS 0.422764 0.898305
54 ASN ARG LEU LEU LEU THR GLY 0.422414 0.827586
55 ACE GLN THR ALA ARG PRK SER THR 0.418605 0.844828
56 ALA GLN THR ALA ARG ALY SER THR 0.415385 0.877193
57 ALA THR PRK ALA ALA ARG LYS SER 0.415254 0.754386
58 MET CYS PRO ARG MET THR ALA VAL MET 0.414966 0.768116
59 THR ARG ARG GLU THR GLN LEU 0.413223 0.859649
60 SER LEU LYS LEU MET THR THR VAL 0.411765 0.793103
61 ALA ARG 9AT 0.41 0.851852
62 LYS ARG ARG ARG LYS SEP CYS GLN ALA NH2 0.40625 0.761905
63 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.406015 0.839286
64 LYS ALA ALA ARG M3L SER ALA 0.404762 0.809524
65 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.403846 0.745455
66 ACE GLN THR ALA ARG BTK SER THR 0.403101 0.877193
67 ALA THR ALY ALA ALA ARG ALY SER ALA PRO 0.402878 0.710145
68 HIS MET THR GLU VAL VAL ARG ARG CYS 0.402778 0.80303
69 ALA ARG TPO LYS 0.401709 0.730159
70 ALA MET ARG VAL 0.4 0.818182
Similar Ligands (3D)
Ligand no: 1; Ligand: GLN 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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