Receptor
PDB id Resolution Class Description Source Keywords
5V8U 2.05 Å EC: 3.4.24.69 SMALL MOLECULE INHIBITOR ABS-143 BOUND TO THE BOTULINUM NEUR SEROTYPE A LIGHT CHAIN CLOSTRIDIUM BOTULINUM METALLOPROTEASE DRUG DESIGN HYDROLASE-HYDROLASE INHIBITOR
Ref.: SMALL MOLECULE METALLOPROTEASE INHIBITOR WITH IN VI VIVO AND IN VIVO EFFICACY AGAINST BOTULINUM NEUROTO SEROTYPE A. TOXICON V. 137 36 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
90M B:502;
A:502;
 Valid;
Valid;
 none;
none;
 submit data
265.307 C12 H12 F N3 O S Cc1c(...
ZN A:501;
B:501;
 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: 90M; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 90M 1 1
2 50C 0.446429 0.685185
3 90J 0.41791 0.925926
Similar Ligands (3D)
Ligand no: 1; Ligand: 90M; Similar ligands found: 165
No: Ligand Similarity coefficient
1 4FC 0.9358
2 J84 0.9301
3 A9B 0.9211
4 HDI 0.9200
5 L02 0.9160
6 NVS 0.9144
7 PB2 0.9127
8 KW7 0.9119
9 72D 0.9115
10 90G 0.9114
11 D26 0.9100
12 1Q1 0.9098
13 HHB 0.9085
14 0NJ 0.9074
15 FCW 0.9064
16 0K7 0.9053
17 FMQ 0.9050
18 HH6 0.9043
19 1R5 0.9043
20 7EH 0.9041
21 6P3 0.9022
22 1Q2 0.9021
23 D25 0.9014
24 PQS 0.9014
25 5DE 0.9009
26 H75 0.9008
27 NIF 0.8996
28 FLP 0.8989
29 PQM 0.8978
30 ZAR 0.8972
31 FMH 0.8960
32 205 0.8960
33 5ZM 0.8960
34 BFL 0.8959
35 RF2 0.8954
36 PTR 0.8947
37 Q8D 0.8947
38 0UL 0.8944
39 Q8G 0.8939
40 4AF 0.8938
41 TID 0.8938
42 122 0.8936
43 S45 0.8936
44 UN3 0.8917
45 121 0.8917
46 4DE 0.8905
47 X6W 0.8902
48 BP5 0.8901
49 C0V 0.8901
50 272 0.8898
51 613 0.8896
52 2OX 0.8890
53 U4J 0.8889
54 1HP 0.8889
55 4CN 0.8881
56 OLU 0.8881
57 CIU 0.8880
58 ENY 0.8876
59 BXZ 0.8842
60 GF7 0.8840
61 15Q 0.8834
62 3C5 0.8830
63 22M 0.8827
64 9FH 0.8826
65 BX4 0.8826
66 JP8 0.8823
67 7G2 0.8822
68 0OK 0.8822
69 0MB 0.8810
70 U55 0.8810
71 KWV 0.8805
72 IPJ 0.8805
73 8V8 0.8799
74 7N8 0.8796
75 GJG 0.8786
76 3DE 0.8785
77 3F4 0.8780
78 LZ4 0.8779
79 Z3R 0.8778
80 28A 0.8777
81 27K 0.8775
82 CT0 0.8774
83 RKN 0.8774
84 G14 0.8771
85 5NR 0.8769
86 3SU 0.8769
87 RGK 0.8764
88 7KE 0.8763
89 25F 0.8762
90 KU1 0.8760
91 0DF 0.8758
92 LC1 0.8757
93 SZ5 0.8756
94 2GE 0.8755
95 CR4 0.8750
96 BMZ 0.8750
97 BXS 0.8746
98 EAA 0.8740
99 5TT 0.8739
100 L1T 0.8733
101 4UE 0.8733
102 DFL 0.8730
103 DFV 0.8726
104 120 0.8726
105 WLH 0.8724
106 P7V 0.8721
107 20D 0.8719
108 L2K 0.8716
109 PIQ 0.8710
110 JTK 0.8710
111 YZ9 0.8710
112 6DQ 0.8708
113 BVS 0.8708
114 TLT 0.8707
115 TVZ 0.8699
116 801 0.8696
117 SO7 0.8693
118 2L7 0.8691
119 A73 0.8687
120 2JX 0.8687
121 NKI 0.8685
122 SNV 0.8681
123 FYR 0.8681
124 1OT 0.8681
125 1V4 0.8673
126 SJR 0.8673
127 AJ1 0.8670
128 1V1 0.8667
129 EQW 0.8666
130 P4L 0.8666
131 08C 0.8664
132 39R 0.8663
133 SWX 0.8660
134 20N 0.8660
135 5C1 0.8654
136 N9M 0.8654
137 F40 0.8649
138 0LO 0.8647
139 6QT 0.8646
140 4UM 0.8646
141 ESJ 0.8644
142 Q0K 0.8644
143 4ZW 0.8640
144 LNN 0.8634
145 6DE 0.8630
146 7L4 0.8627
147 AJG 0.8618
148 4AU 0.8615
149 SSY 0.8613
150 1SF 0.8612
151 0RA 0.8610
152 1XS 0.8609
153 JON 0.8609
154 27F 0.8599
155 PRL 0.8599
156 8D6 0.8596
157 YE6 0.8588
158 EAE 0.8587
159 3CX 0.8585
160 CUE 0.8578
161 AO 0.8577
162 7FU 0.8570
163 JTE 0.8569
164 51Y 0.8534
165 43G 0.8528
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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