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 (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: GLN ARG ALA THR LYS MET NH2; Similar ligands found: 80
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 0.876405 0.963636
3 ACE CSO ARG ALA THR LYS MET LEU 0.614035 0.84375
4 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.571429 0.854839
5 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.550459 0.890909
6 ALA ARG THR LYS GLN THR ALA ARG 0.545455 0.890909
7 ALA ARG THR LYS GLN THR ALA ARG LYS 0.545455 0.890909
8 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.525862 0.929825
9 GLU ALA GLN THR ARG LEU 0.522523 0.857143
10 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.516949 0.84127
11 MET ABA LEU ARG MET THR ALA VAL MET 0.516949 0.912281
12 GLN THR ALA ARG M3L SER THR GLY 0.516667 0.84127
13 MET CYS LEU ARG MET THR ALA VAL MET 0.504132 0.912281
14 GLU ALA THR GLN LEU MET ASN 0.5 0.785714
15 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.495652 0.842105
16 ASN ARG LEU MET LEU THR GLY 0.491228 0.896552
17 MET CYS LEU ARG NLE THR ALA VAL MET 0.488 0.896552
18 ALA ARG THR M3L GLN THR ALA ARG 0.482759 0.84127
19 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.482759 0.946429
20 GLN ARG SER THR SEP THR 0.482456 0.734375
21 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.478261 0.859649
22 ALA ARG THR MLY GLN THR ALA ARG LYS 0.470588 0.883333
23 GLU ARG GLY MET THR 0.464286 0.892857
24 ALA ARG THR MLY GLN 0.463636 0.883333
25 ARG ARG GLY MET NH2 0.460784 0.821429
26 ARG ARG ALA ALA 0.458333 0.732143
27 ARG ARG ARG GLU THR GLN VAL 0.457944 0.839286
28 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.457364 0.854839
29 ALA ARG THR ALY GLN THR ALA 0.45614 0.892857
30 ALA ALA LEU THR ARG ALA 0.454545 0.854545
31 ACE ALA ARG THR LYS GLN 0.453704 0.888889
32 LYS MET ASN THR GLN PHE THR ALA VAL 0.450382 0.770492
33 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.448276 0.963636
34 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.447917 0.732143
35 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.442478 0.898305
36 LYS ARG LYS 0.442105 0.745455
37 THR ILE MET MET GLN ARG GLY 0.440678 0.929825
38 ALA ARG THR MLY GLN THR ALA 0.439655 0.883333
39 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.439655 0.883333
40 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.439655 0.854839
41 ALA ARG THR M3L GLN THR ALA 0.439655 0.854839
42 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.439655 0.854839
43 MET ALA ARG 0.438776 0.836364
44 THR ARG ARG GLU THR GLN LEU 0.438596 0.859649
45 LEU GLU LYS ALA ARG GLY SER THR TYR 0.43662 0.769231
46 GLU LEU ARG ARG LYS MET MET TYR MET 0.436508 0.809524
47 ALA ARG THR M3L GLN THR ALA ARG LYS 0.435897 0.854839
48 ALA GLN THR ALA ARG ALY SER THR 0.435484 0.877193
49 ACE GLN THR ALA ARG KCR SER THR 0.434109 0.844828
50 ARG ASP ARG ALA ALA LYS LEU 0.433962 0.785714
51 SER LEU LYS LEU MET THR THR VAL 0.432432 0.775862
52 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.431193 0.854545
53 ALA ARG THR MLY GLN THR ALA ARG TYR 0.427481 0.791045
54 GLU LEU LYS ARG LYS MET ILE TYR MET 0.426471 0.809524
55 LYS ARG LYS ARG LYS ARG LYS ARG 0.425743 0.727273
56 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.42446 0.854839
57 LYS ALA ARG VAL LEU ALA GLU ALA MET 0.424 0.839286
58 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.424 0.839286
59 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.423077 0.763636
60 ALA THR PRK ALA ALA ARG LYS SER 0.419643 0.736842
61 01W ARG TRP THR DAB MET LEU GLY 0.418301 0.626506
62 LYS THR LYS LEU LEU 0.413462 0.732143
63 GLN VAL PRO LEU ARG PRO MET THR TYR LYS 0.4125 0.72973
64 ARG GLU ALA ALA 0.411765 0.763636
65 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.410714 0.862069
66 GLU LEU ASN ARG LYS MET ILE TYR MET 0.409722 0.828125
67 LYS ALA VAL PHE ASN PHE ALA THR MET 0.409091 0.730159
68 LYS ALA VAL TYR ASN LEU ALA THR MET 0.408759 0.71875
69 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.408163 0.745455
70 ACE ALA ARG THR GLU VAL TYR NH2 0.408 0.758065
71 LYS GLN THR ALA ARG M3L SER THR GLY 0.406504 0.84127
72 LEU PRO PHE GLU ARG ALA THR VAL MET 0.406452 0.771429
73 ARG ARG PHE AIB ALA MET LEU ALA 0.406015 0.786885
74 LEU LYS THR LYS LEU LEU 0.40566 0.732143
75 LYS ALA LEU TYR ASN PHE ALA THR MET 0.402878 0.69697
76 ALA ARG LYS LEU ASP 0.401869 0.821429
77 PHE TYR ARG ALA LEU MET 0.401515 0.75
78 MET ARG THR GLY ASN ALA SNN 0.4 0.787879
79 ALA MET ARG VAL 0.4 0.818182
80 LYS ALA PRO ARG ALY GLN LEU ALA THR LYS 0.4 0.73913
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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