Receptor
PDB id Resolution Class Description Source Keywords
3DS9 1.76 Å EC: 3.4.24.69 A POTENT PEPTIDOMIMETIC INHIBITOR OF BOTULINUM NEUROTOXIN SEROTYPE A HAS A VERY DIFFERENT CONFORMATION THAN SNAP-25 S UBSTRATE CLOSTRIDIUM BOTULINUM SNARE BOTULISM INHIBITION METALLOPROTEASE NEUROTRANSMISSION NEUROMUSCULAR JUNCTION HYDROLASE MEMBRANE METAL-BINDING NEUROTOXIN PHARMACEUTICAL PROTEASE SECRETED TOXIN TRANSMEMBRANE ZINC
Ref.: A POTENT PEPTIDOMIMETIC INHIBITOR OF BOTULINUM NEUROTOXIN SEROTYPE A HAS A VERY DIFFERENT CONFORMATION THAN SNAP-25 SUBSTRATE STRUCTURE V. 16 1588 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
01W ARG TRP THR DAB MET LEU GLY B:197;
 Valid;
 none;
 submit data
1075.26 n/a S(CCC...
NI A:601;
 Part of Protein;
 none;
 submit data
58.693 Ni [Ni+2...
ZN A:500;
 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: 01W ARG TRP THR DAB MET LEU GLY; Similar ligands found: 39
No: Ligand ECFP6 Tc MDL keys Tc
1 01W ARG TRP THR DAB MET LEU GLY 1 1
2 ARG ARG ARG TRP ARG ARG LEU THR VAL 0.572368 0.743902
3 LYS ARG TRP ILE ILE MET GLY LEU ASN LYS 0.510989 0.72093
4 SER ARG TYR TRP ALA ILE ARG THR ARG 0.482955 0.709302
5 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.48125 0.707317
6 ALA ASN SER ARG TRP GLN ASP THR ARG LEU 0.48 0.738095
7 SER LEU LEU MET TRP ILE THR GLN LEU 0.479042 0.670588
8 SER LEU LEU MET TRP ILE THR GLN SER 0.47619 0.670588
9 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.475904 0.698795
10 SER LEU LEU MET TRP ILE THR GLN ALA 0.473373 0.670588
11 ARG ARG ARG ARG TRP ARG GLU ARG GLN 0.471338 0.638554
12 SER LEU LEU MET TRP ILE THR GLN CYS 0.467836 0.670588
13 ALA ASN SER ARG TRP GLN VAL THR ARG VAL 0.467066 0.72619
14 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.464706 0.690476
15 ARG LEU TRP SER 0.464052 0.674699
16 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS 0.461538 0.674419
17 SER ARG ARG TRP ARG ARG TRP ASN ARG 0.461538 0.690476
18 SER SER THR ARG GLY ILE SER GLN LEU TRP 0.458564 0.697674
19 SER LEU LEU MET TRP ILE THR GLN VAL 0.456647 0.678571
20 ARG PHE MET ASP TYR TRP GLU GLY LEU 0.449198 0.72093
21 ALA ASN SER ARG TRP GLN THR SER ILE ILE 0.446927 0.705882
22 GLU LEU ARG SER ARG TYR TRP ALA ILE 0.442623 0.712644
23 GLU LEU ASP NRG TRP ALA SER 0.435028 0.788235
24 ALA ASN SER ARG TRP ALY THR SER ILE ILE 0.434783 0.72093
25 MET SER LEU PRO GLY ARG TRP LYS PRO LYS 0.425743 0.752809
26 MET ABA LEU ARG MET THR ALA VAL MET 0.420732 0.638554
27 LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.416244 0.696629
28 ALA ASN SER ARG TRP PRO THR THR ARG LEU 0.413978 0.730337
29 ALA SER ASN GLU ASN TRP GLU THR MET 0.411765 0.678571
30 MET LEU ILE TYR SER MET TRP GLY LYS 0.411458 0.662921
31 ARG ARG ALA THR LYS MET NH2 0.407643 0.646341
32 GLU GLU TYR LEU LYS ALA TRP THR PHE 0.407407 0.639535
33 ARG PHE PRO LEU THR PHE GLY TRP CYS PHE 0.406863 0.75
34 MET LEU TRP GLY TYR LEU GLN TYR VAL 0.405556 0.639535
35 ARG PHE PRO LEU THR PHE GLY TRP 0.405128 0.727273
36 MET CYS LEU ARG MET THR ALA VAL MET 0.404762 0.658537
37 GLY LEU MET TRP LEU SER TYR PHE VAL 0.404494 0.655172
38 ASN ARG LEU MET LEU THR GLY 0.403846 0.650602
39 ARG ARG PHE AIB ALA MET LEU ALA 0.403509 0.638554
Similar Ligands (3D)
Ligand no: 1; Ligand: 01W ARG TRP THR DAB MET LEU GLY; 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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