Receptor
PDB id Resolution Class Description Source Keywords
3NF3 2.4 Å EC: 3.4.24.69 CRYSTAL STRUCTURE OF BONT/A LC WITH JTH-NB-7239 PEPTIDE CLOSTRIDIUM BOTULINUM BOTULINUM NEUROTOXIN SNARE BOTULISM INHIBITION METALLOPRNEUROTRANSMISSION NEUROMUSCULAR JUNCTION HYDROLASE MEMBRMETAL-BINDING PROTEASE SECRETED TOXIN HYDROLASE-HYDROLAINHIBITOR COMPLEX
Ref.: ITERATIVE STRUCTURE-BASED PEPTIDE-LIKE INHIBITOR DE AGAINST THE BOTULINUM NEUROTOXIN SEROTYPE A. PLOS ONE V. 5 E1137 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG ARG PHE AIB ALA MET LEU ALA C:1;
Valid;
none;
Ki = 638 nM
883.178 n/a S(CCC...
NI A:700;
Part of Protein;
none;
submit data
58.693 Ni [Ni+2...
ZN A:600;
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 PHE AIB ALA MET LEU ALA; Similar ligands found: 42
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG ARG PHE AIB ALA MET LEU ALA 1 1
2 ACE ALC ARG ALA MET CY1 SER LEU NH2 0.559702 0.83871
3 ARG ARG LEU ILE PHE NH2 0.512195 0.821429
4 PHE TYR ARG ALA LEU MET 0.507463 0.822581
5 GLU LEU ARG ARG LYS MET MET TYR MET 0.477612 0.854839
6 ARG ARG ALA THR LYS MET NH2 0.460317 0.816667
7 PHE ARG TYR LEU GLY 0.458015 0.734375
8 SER GLU ILE GLU PHE ALA ARG LEU 0.457143 0.758065
9 ARG HIS LYS ALY LEU MET PHE LYS 0.456376 0.769231
10 ARG MET PHE PRO ASN ALA PRO TYR LEU 0.45625 0.670886
11 ACE ALC ARG MPQ MET ALA SER TBG NH2 0.439189 0.815385
12 SER SER ILE GLU PHE ALA ARG LEU 0.4375 0.774194
13 ARG PHE MET ASP TYR TRP GLU GLY LEU 0.435583 0.71831
14 ACE PHE LYS PHE TA2 ALA LEU ARG NH2 0.435374 0.75
15 ARG ARG GLY MET NH2 0.431034 0.807018
16 PHE ARG SER LYS GLY GLU GLU LEU PHE THR 0.430464 0.738462
17 VAL MET ALA PRO ARG THR LEU PHE LEU 0.43038 0.712329
18 01W ARG TRP THR DAB MET LEU GLY 0.426829 0.638554
19 ARG ARG GLY LEU NH2 0.426087 0.754386
20 GLU LEU LYS ARG LYS MET ILE TYR MET 0.425676 0.825397
21 ACE ARG ARG B3L MEA NH2 0.423077 0.761905
22 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.418919 0.753846
23 VAL ALA PHE ARG SER 0.418605 0.807018
24 ARG ILE PHE SER 0.418605 0.793103
25 LYS MET ASN THR GLN PHE THR ALA VAL 0.417808 0.730159
26 ASN ARG LEU MET LEU THR GLY 0.416667 0.790323
27 LEU PRO PHE GLU ARG ALA THR VAL MET 0.415663 0.712329
28 ARG ABA PHE ILE PHE ALA ASN ILE 0.414286 0.714286
29 GLU GLU ASN LEU LEU ASP PHE VAL ARG PHE 0.412162 0.746032
30 ARG VAL LEU PHE GLU ALA MET 0.410959 0.87931
31 LYS MET ASP SEP PHE LEU ASP MET GLN LEU 0.410596 0.691176
32 ARG ARG LEU PRO ILE PHE SER ARG LEU 0.410256 0.671233
33 GLU LEU ASN ARG LYS MET ILE TYR MET 0.410256 0.787879
34 MET ABA LEU ARG MET THR ALA VAL MET 0.410072 0.803279
35 ACE ALC ARG ALA ODA SER LEU NH2 0.408805 0.620253
36 LEU PRO PHE GLU ARG ALA THR ILE MET 0.408284 0.702703
37 GLN ARG ALA THR LYS MET NH2 0.406015 0.786885
38 ARG PRO MET THR PHE LYS GLY ALA LEU 0.404762 0.702703
39 PHE LEU ARG GLY ARG ALA TYR GLY LEU 0.40411 0.75
40 LEU PRO PHE ASP ARG THR THR ILE MET 0.402439 0.716216
41 MET CYS LEU ARG MET THR ALA VAL MET 0.401408 0.833333
42 SER SER LEU GLU ASN PHE ARG ALA TYR VAL 0.4 0.705882
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
Feedback