Receptor
PDB id Resolution Class Description Source Keywords
2G7Q 2.41 Å EC: 3.4.24.69 STRUCTURE OF THE LIGHT CHAIN OF BOTULINUM NEUROTOXIN SEROTYP TO SMALL MOLECULE INHIBITORS CLOSTRIDIUM BOTULINUM BOTULINUM NEUROTOXIN ZINC PROTEASE SNAP25 HYDROLASE
Ref.: LIGHT CHAIN OF BOTULINUM NEUROTOXIN SEROTYPE A: STR RESOLUTION OF A CATALYTIC INTERMEDIATE. BIOCHEMISTRY V. 45 8903 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AHL A:500;
Valid;
none;
submit data
189.216 C6 H15 N5 O2 [H]/N...
ZN A:452;
B:451;
Part of Protein;
Part of Protein;
none;
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: AHL; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 AHL 1 1
2 8SZ 0.5 0.822222
3 HRG 0.488889 0.638298
4 HAR 0.468085 0.787234
5 G3M 0.468085 0.62
6 1OV 0.466667 0.627451
7 AAG 0.42 0.66
8 NMM 0.408163 0.612245
Similar Ligands (3D)
Ligand no: 1; Ligand: AHL; Similar ligands found: 218
No: Ligand Similarity coefficient
1 ARG 0.9544
2 CIR 0.9437
3 GGB 0.9400
4 MLY 0.9354
5 J9Y 0.9352
6 NPI 0.9342
7 6HN 0.9320
8 MLZ 0.9301
9 IAR 0.9237
10 ILO 0.9215
11 4JK 0.9185
12 EXY 0.9184
13 JX7 0.9170
14 M3L 0.9157
15 GVA 0.9133
16 DAR 0.9096
17 N8C 0.9089
18 26P 0.9081
19 GRQ 0.9070
20 API 0.9063
21 E8U 0.9040
22 RGP 0.9023
23 UN1 0.9015
24 5KJ 0.9007
25 9YT 0.9006
26 T03 0.9006
27 NNH 0.9003
28 WT2 0.9001
29 14W 0.8998
30 KNA 0.8998
31 ALY 0.8991
32 DHH 0.8990
33 DX5 0.8985
34 I2E 0.8983
35 NFZ 0.8982
36 PML 0.8978
37 XRX 0.8968
38 KAP 0.8965
39 GGG 0.8963
40 4Z0 0.8957
41 7XA 0.8951
42 ENV 0.8950
43 58X 0.8942
44 ZZU 0.8936
45 DXG 0.8935
46 6FG 0.8935
47 6C4 0.8932
48 2NP 0.8923
49 LYS 0.8920
50 RED 0.8920
51 4DI 0.8919
52 HLP 0.8919
53 GNW 0.8914
54 2OR 0.8912
55 PAN 0.8909
56 2FM 0.8908
57 S7V 0.8908
58 MF3 0.8908
59 DA3 0.8908
60 5TO 0.8903
61 NOT 0.8900
62 N9J 0.8900
63 HJD 0.8898
64 6C5 0.8895
65 I58 0.8894
66 SPD 0.8892
67 CLT 0.8890
68 3KJ 0.8890
69 GLY GLY GLY 0.8886
70 KLS 0.8878
71 OOG 0.8875
72 LPA 0.8874
73 37Z 0.8873
74 SLZ 0.8872
75 IVL 0.8868
76 OJD 0.8867
77 5SP 0.8867
78 0XR 0.8865
79 ENW 0.8865
80 FB6 0.8859
81 KPV 0.8859
82 VUR 0.8853
83 TZM 0.8853
84 11C 0.8850
85 R5P 0.8850
86 PJL 0.8845
87 DKA 0.8844
88 Z70 0.8842
89 L06 0.8841
90 FXY 0.8837
91 XOG 0.8835
92 DA2 0.8831
93 PA5 0.8828
94 1AJ 0.8828
95 DLY 0.8824
96 6C9 0.8814
97 5UF 0.8814
98 9VQ 0.8813
99 3IP 0.8813
100 PZX 0.8811
101 TEG 0.8806
102 DIR 0.8806
103 3H2 0.8804
104 4BX 0.8804
105 7VY 0.8802
106 P93 0.8802
107 8AC 0.8798
108 SZA 0.8798
109 BZM 0.8795
110 DMA 0.8792
111 8CV 0.8790
112 NWH 0.8787
113 LL2 0.8786
114 JPQ 0.8785
115 ONH 0.8782
116 H35 0.8779
117 HPP 0.8779
118 N9M 0.8779
119 5RP 0.8777
120 IPE 0.8776
121 AHC 0.8774
122 DLT 0.8773
123 5PV 0.8771
124 SB9 0.8770
125 QH3 0.8770
126 IJ6 0.8770
127 PPT 0.8767
128 DNN 0.8767
129 6FR 0.8764
130 JM2 0.8764
131 7OD 0.8763
132 HGA 0.8762
133 TYR 0.8761
134 OCA 0.8761
135 TOH 0.8761
136 7R4 0.8760
137 LPB 0.8758
138 PMV 0.8757
139 0A9 0.8753
140 MJW 0.8752
141 3EB 0.8749
142 LVD 0.8747
143 E79 0.8743
144 4Z9 0.8742
145 0V7 0.8742
146 ISY 0.8740
147 HHV 0.8739
148 GLR 0.8734
149 2J3 0.8727
150 SB7 0.8720
151 3IL 0.8712
152 PH3 0.8709
153 G6Q 0.8706
154 011 0.8705
155 ENO 0.8700
156 9J6 0.8697
157 S0F 0.8696
158 J4K 0.8693
159 EGV 0.8693
160 IJ1 0.8692
161 1N5 0.8691
162 IPR 0.8687
163 A8K 0.8686
164 O45 0.8684
165 DTY 0.8682
166 REL 0.8674
167 FHC 0.8671
168 64Z 0.8671
169 YPN 0.8670
170 GZ2 0.8669
171 37E 0.8666
172 PHE 0.8665
173 JF5 0.8658
174 MMS 0.8657
175 3CX 0.8656
176 S7D 0.8655
177 S0B 0.8654
178 DAH 0.8653
179 RQD 0.8651
180 C82 0.8650
181 3GZ 0.8645
182 RK4 0.8645
183 5OY 0.8644
184 F6P 0.8643
185 A5P 0.8641
186 VIO 0.8639
187 F98 0.8638
188 3IB 0.8631
189 1HR 0.8629
190 YOF 0.8628
191 L22 0.8626
192 HPO 0.8624
193 PAL 0.8621
194 CUW 0.8616
195 GHQ 0.8615
196 531 0.8613
197 C4E 0.8613
198 6MW 0.8612
199 JKK 0.8610
200 D2G 0.8608
201 LYN 0.8607
202 HSA 0.8595
203 DST 0.8595
204 VJJ 0.8595
205 6XA 0.8588
206 6PG 0.8586
207 0V8 0.8581
208 C0H 0.8581
209 6PR 0.8577
210 CUT 0.8570
211 19N 0.8566
212 QBM 0.8564
213 PBN 0.8563
214 2UB 0.8560
215 2UZ 0.8559
216 HNE 0.8541
217 536 0.8531
218 4BF 0.8529
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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