Receptor
PDB id Resolution Class Description Source Keywords
3BOO 1.4 Å EC: 3.4.24.69 STRUCTURE OF THE C. BOTULINUM NEUROTOXIN SEROTYPE A WITH AN PEPTIDE BOUND CLOSTRIDIUM BOTULINUM BOTULINUM NEUROTOXIN METALLOPROTEASE PEPTIDIC INHIBITOR TOXIN INHIBITOR COMPLEX
Ref.: CATALYTIC FEATURES OF THE BOTULINUM NEUROTOXIN A LI REVEALED BY HIGH RESOLUTION STRUCTURE OF AN INHIBIT PEPTIDE COMPLEX. BIOCHEMISTRY V. 47 5736 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACE CSO ARG ALA THR LYS MET LEU B:0;
 Valid;
 none;
 Ki = 1.9 uM
881.111 n/a S(O)C...
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: ACE CSO ARG ALA THR LYS MET LEU; Similar ligands found: 74
No: Ligand ECFP6 Tc MDL keys Tc
1 ACE CSO ARG ALA THR LYS MET LEU 1 1
2 ARG ARG ALA THR LYS MET NH2 0.622807 0.84375
3 GLN ARG ALA THR LYS MET NH2 0.583333 0.84375
4 ACE GLU ALA GLN THR ARG LEU 0.567797 0.796875
5 MET ABA LEU ARG MET THR ALA VAL MET 0.539062 0.830769
6 MET CYS LEU ARG MET THR ALA VAL MET 0.526718 0.859375
7 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.508065 0.769231
8 ARG ASP ARG ALA ALA LYS LEU 0.504425 0.71875
9 MET CYS LEU ARG NLE THR ALA VAL MET 0.503704 0.846154
10 GLU ALA GLN THR ARG LEU 0.5 0.78125
11 ALA MET ALA PRO ARG THR LEU LEU LEU 0.49635 0.736842
12 ILE LEU ASN ALA MET ILE THR LYS ILE 0.492308 0.757576
13 ASN ARG LEU MET LEU THR GLY 0.487805 0.846154
14 THR SER ARG HIS LYS ALY LEU MET ALA 0.482759 0.77027
15 THR ARG ARG GLU THR GLN LEU 0.479339 0.8125
16 GLU LEU LYS ARG LYS MET ILE TYR MET 0.479167 0.746479
17 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.477273 0.826087
18 LYS THR LYS LEU LEU 0.468468 0.703125
19 GLU LEU ARG ARG LYS MET MET TYR MET 0.467153 0.771429
20 SER LEU LYS LEU MET THR THR VAL 0.466667 0.753846
21 ALA ARG THR LYS GLN THR ALA ARG LYS 0.460938 0.78125
22 ALA ARG LYS LEU ASP 0.46087 0.75
23 LEU LYS THR LYS LEU LEU 0.460177 0.703125
24 THR ARG SER GLY ALY VAL MET ARG ARG LEU 0.453846 0.784615
25 ACE ALA ARG THR LYS GLN 0.453782 0.75
26 VAL MET ALA PRO ARG ALA LEU LEU LEU 0.453237 0.671053
27 GLU LEU ASN ARG LYS MET ILE TYR MET 0.45098 0.763889
28 ALA ALA LEU THR ARG ALA 0.45 0.75
29 ACE ALC ARG ALA MET CY1 SER LEU NH2 0.448276 0.785714
30 LEU GLU LYS ALA ARG GLY SER THR TYR 0.444444 0.736111
31 ASN PRO ARG ALA MET GLN ALA LEU LEU 0.444444 0.688312
32 GLN ILE LYS VAL ARG VAL ASP MET VAL 0.442029 0.8
33 ALA ARG THR M3L GLN THR ALA ARG 0.44186 0.826087
34 GLU ALA THR GLN LEU MET ASN 0.440945 0.71875
35 ARG PRO MET THR TYR LYS GLY ALA LEU 0.439759 0.703704
36 THR ILE MET MET GLN ARG GLY 0.4375 0.818182
37 ILE LEU MET GLU HIS ILE HIS LYS LEU 0.43662 0.613333
38 ALA ARG THR LYS GLN THR ALA ARG 0.434426 0.765625
39 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.434109 0.80303
40 ARG PRO MET THR PHE LYS GLY ALA LEU 0.433735 0.730769
41 VAL MET ALA PRO ARG THR LEU PHE LEU 0.433121 0.717949
42 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.430769 0.8125
43 ALA ARG THR GLU LEU TYR ARG SER LEU 0.429577 0.732394
44 ILE LEU ASN ALA MET ILE ALA LYS ILE 0.427481 0.69697
45 PHE TYR ARG ALA LEU MET 0.425532 0.694444
46 GLY GLY ARG LYS LYS TYR LYS LEU 0.425373 0.690141
47 GLY GLY LYS LYS LYS TYR ARG LEU 0.425373 0.690141
48 GLY GLY LYS LYS ARG TYR LYS LEU 0.425373 0.690141
49 LEU PRO PHE GLU ARG ALA THR ILE MET 0.424242 0.708861
50 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.423358 0.765625
51 GLY THR LEU SER ASN ARG ALA SER LYS LEU 0.421053 0.661538
52 MET CYS PRO ARG MET THR ALA VAL MET 0.421053 0.736842
53 ALA ARG THR M3L GLN THR ALA ARG LYS 0.420635 0.797101
54 LYS ALA PRO ARG ALY GLN LEU ALA THR LYS 0.419355 0.710526
55 ILE LEU ASN ALA MET ILE VAL LYS ILE 0.419118 0.69697
56 ALA ARG THR MLY GLN 0.416 0.835821
57 SER GLU LEU GLU ILE LYS ARG TYR 0.413793 0.722222
58 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.412281 0.65625
59 ILE LEU ALA LYS PHE LEU HIS THR LEU 0.412162 0.605263
60 LEU PRO PHE GLU ARG ALA THR VAL MET 0.412121 0.717949
61 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.41129 0.784615
62 HIS MET THR GLU VAL VAL ARG ARG CYS 0.409396 0.767123
63 ALA MET ARG VAL 0.408696 0.71875
64 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.408333 0.734375
65 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.408163 0.618421
66 LYS PRO VAL LEU ARG THR ALA 0.406897 0.671053
67 ASN ARG LEU LEU LEU THR GLY 0.406504 0.784615
68 ACE GLN THR ALA ARG PRK SER THR 0.404412 0.746269
69 ALA ARG THR MLY GLN THR ALA ARG TYR 0.402778 0.780822
70 ARG HIS LYS ALY LEU MET PHE LYS 0.402597 0.653333
71 ALA GLN THR ALA ARG ALY SER THR 0.40146 0.8
72 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.4 0.65625
73 SER GLU ILE GLU PHE ALA ARG LEU 0.4 0.710145
74 ALA THR ALY ALA ALA ARG ALY SER ALA PRO 0.4 0.662338
Similar Ligands (3D)
Ligand no: 1; Ligand: ACE CSO ARG ALA THR LYS MET LEU; 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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