Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG ARG GLY CYS NH2 B:500;
Valid;
none;
Ki = 157 nM
493.638 n/a SCC(N...
NA B:453;
Invalid;
none;
submit data
22.99 Na [Na+]
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 GLY CYS NH2; Similar ligands found: 25
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG ARG GLY CYS NH2 1 1
2 ARG ARG GLY LEU NH2 0.753623 0.891304
3 ARG ARG GLY MET NH2 0.732394 0.875
4 ARG ARG GLY ILE NH2 0.680556 0.891304
5 SER GLY ARG GLY LYS NH2 0.565789 0.8
6 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.528571 0.866667
7 GLU ARG GLY SER GLY ARG 0.517241 0.82
8 ARG ARG ARG ARG ARG ARG ARG ARG 0.493333 0.906977
9 GLU ARG GLY MET THR 0.483871 0.773585
10 ARG ARG ALA ALA 0.480519 0.847826
11 LYS ARG LYS 0.460526 0.826087
12 ARG ASP 0.457143 0.844444
13 ARG GLY THR 0.454545 0.833333
14 ARG SER ARG 0.453333 0.795918
15 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.448718 0.847826
16 ARG GLU 0.444444 0.863636
17 ARG GLY ASP 0.435897 0.888889
18 ARG LEU GLY GLU SER 0.423077 0.847826
19 GLY ARG GLY ASP SER PRO 0.422222 0.833333
20 LYS ARG LYS ARG LYS ARG LYS ARG 0.421687 0.886364
21 ARG VAL 0.416667 0.765957
22 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.405941 0.8
23 ARG GLU ALA ALA 0.404762 0.847826
24 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.402299 0.808511
25 LEU TYR LEU VAL CYS GLY GLU ARG GLY 0.4 0.719298
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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