Receptor
PDB id Resolution Class Description Source Keywords
3C8A 1.52 Å EC: 3.4.24.69 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEURO SEROTYPE A WITH INHIBITORY PEPTIDE RRGL CLOSTRIDIUM BOTULINUM BOTULINUM NEUROTOXIN TYPE A CATALYTIC DOMAIN ENDOPEPTIDASEWARFARE AGENT METALLOPROTEASE PROTEASE SECRETED HYDROLAHYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURE- AND SUBSTRATE-BASED INHIBITOR DESIGN FOR CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPE A J.BIOL.CHEM. V. 283 18883 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG ARG GLY LEU NH2 B:500;
Valid;
none;
Ki = 660 nM
503.653 n/a O=C(N...
SO4 A:451;
A:452;
A:453;
Invalid;
Invalid;
Invalid;
none;
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 GLY LEU NH2; Similar ligands found: 41
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG ARG GLY LEU NH2 1 1
2 ARG ARG GLY CYS NH2 0.753623 0.891304
3 ARG ARG GLY MET NH2 0.75 0.86
4 ARG ARG GLY ILE NH2 0.69863 0.956522
5 SER GLY ARG GLY LYS NH2 0.564103 0.788462
6 ARG LEU GLY GLU SER 0.52 0.955556
7 GLU ARG GLY SER GLY ARG 0.516854 0.773585
8 GLU ARG GLY MET THR 0.516129 0.796296
9 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.506849 0.8125
10 ARG ARG ALA ALA 0.5 0.87234
11 ALA ARG LYS LEU ASP 0.476744 0.86
12 ARG ARG ARG ARG ARG ARG ARG ARG 0.474359 0.847826
13 ARG GLY THR 0.474359 0.82
14 LYS ARG LYS 0.461538 0.77551
15 ARG ARG LEU ILE PHE NH2 0.46 0.877551
16 ARG SER ARG 0.454545 0.75
17 ARG GLY TYR LEU TYR GLN GLY LEU 0.453704 0.77193
18 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.45 0.795918
19 ARG ASP ARG ALA ALA LYS LEU 0.449438 0.857143
20 ARG ARG LEU LEU ARG GLY HIS ASN GLN TYR 0.44 0.692308
21 ARG ASP 0.438356 0.791667
22 ARG VAL 0.438356 0.829787
23 PHE LEU ARG GLY ARG ALA TYR GLY LEU 0.434783 0.789474
24 ARG GLY TYR VAL TYR GLN GLY LEU 0.433628 0.77193
25 ARG GLU 0.426667 0.808511
26 ARG ARG PHE AIB ALA MET LEU ALA 0.426087 0.754386
27 ARG ARG ALA THR LYS MET NH2 0.425743 0.736842
28 ARG GLU ALA ALA 0.423529 0.87234
29 LYS ARG LYS ARG LYS ARG LYS ARG 0.423529 0.829787
30 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.421569 0.86
31 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.420455 0.87234
32 ARG GLY ASP 0.419753 0.833333
33 ARG ASP ALA ALA 0.414634 0.833333
34 LEU TYR LEU VAL CYS GLY GLU ARG GLY 0.413223 0.77193
35 GLY ARG GLY ASP SER PRO 0.408602 0.784314
36 SER ARG ILE ARG ILE ARG GLY TYR VAL ARG 0.401709 0.737705
37 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.4 0.830189
38 PHE LEU ARG GLY ARG ALA TYR VAL LEU 0.4 0.789474
39 ASN ARG LEU MET LEU THR GLY 0.4 0.77193
40 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.4 0.685185
41 THR ALA ARG M3L SER THR 0.4 0.716667
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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