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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: 33
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG ARG GLY CYS NH2 1 1
2 ARG ARG GLY LEU NH2 0.757576 0.87234
3 ARG ARG GLY MET NH2 0.714286 0.857143
4 ARG ARG GLY ILE NH2 0.695652 0.87234
5 SER GLY ARG GLY LYS NH2 0.60274 0.82
6 GLU ARG GLY SER GLY ARG 0.517241 0.84
7 ARG ARG ARG ARG ARG ARG ARG ARG 0.513514 0.886364
8 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.513514 0.886364
9 ARG ARG ALA ALA 0.5 0.829787
10 GLU ARG GLY MET THR 0.494505 0.759259
11 ARG GLY THR 0.493333 0.816327
12 ARG SER ARG 0.493151 0.816327
13 LYS ARG LYS 0.486842 0.808511
14 ARG GLY ASP 0.473684 0.869565
15 ARG GLU 0.464789 0.866667
16 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.463415 0.866667
17 ARG LEU GLY GLU SER 0.447368 0.829787
18 GLY ARG GLY ASP SER PRO 0.438202 0.816327
19 ALA ARG 0.434783 0.804348
20 ARG ARG LEU ILE PHE NH2 0.428571 0.764706
21 ARG GLY ARG ALA 2MR GLY GLN GLU 0.424242 0.854167
22 PRO PRO LYS LYS LYS ARG LYS VAL 0.423529 0.791667
23 THR ALA ARG M3L SER THR 0.423529 0.629032
24 ARG VAL 0.422535 0.770833
25 ARG GLU ALA ALA 0.421687 0.829787
26 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.421053 0.607143
27 ARG ARG ARG VAL ARG 00S 0.419355 0.784314
28 ARG ASP ALA ALA 0.4125 0.829787
29 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.411765 0.784314
30 ARG ASP 0.410959 0.847826
31 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.409091 0.791667
32 ALA ARG 9AT 0.407895 0.78
33 ARG ARG ALA THR LYS MET NH2 0.401961 0.732143
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: 119
This union binding pocket(no: 1) in the query (biounit: 3c88.bio1) has 46 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 3AQT RCO 1.22449
3 1KAP GLY SER ASN SER 1.38889
4 5WJ6 B4A 1.38889
5 5MTE BB2 1.45985
6 2J83 BAT 1.52672
7 3DWB RDF 1.62037
8 5KD8 TNR 1.85185
9 3O01 DXC 1.94805
10 2UXR ICT 1.99005
11 2NV4 SAM 2.04082
12 1RJW ETF 2.0649
13 5ZI7 GLU 2.08333
14 3N75 G4P 2.08333
15 6GSG RCO 2.08877
16 5AMC GLY NIY 2.31481
17 4BXK 1IU 2.31481
18 4KSY 1SY 2.47934
19 3VPD CIT 2.4911
20 2YB9 HA0 2.5463
21 3M6P BB2 2.59067
22 4ISS TAR 2.63975
23 1Y79 LYS TRP 2.77778
24 5IUY BOG 2.77778
25 5N6N SUC 2.77778
26 4B6C B5U 3.06122
27 5KDX GAL TNR 3.24074
28 4B52 RDF 3.28947
29 3FW3 GLC 3.38346
30 6BTN E8M 3.46535
31 6BTQ E8S 3.46535
32 6H1U ASP 3.48432
33 4JE7 BB2 3.5533
34 2OKL BB2 3.78378
35 3G5K BB2 3.82514
36 4DD8 BAT 3.84615
37 5LX9 OLB 3.87324
38 1BKC INN 3.90625
39 1ATL 0QI 3.9604
40 1W6U HXC 3.97351
41 1QJI PKF 4
42 2ZX2 RAM 4.10256
43 5NM7 GLY 4.13534
44 5IM3 DTP 4.16667
45 5WHT SIA GAL 4.34783
46 3RZ3 U94 4.37158
47 3ZVS MLI 4.375
48 5CHR 4NC 4.37956
49 2ZXG S23 4.39815
50 4TVD BGC 4.39815
51 4GAA BES 4.39815
52 2JHP GUN 4.39815
53 4KX8 L2O VAL VAL ASP 4.39815
54 1S17 GNR 4.44444
55 2W14 WR2 4.45545
56 3F5A SIA GAL NAG 4.47154
57 4AIG FLX 4.47761
58 3SBZ MLI 4.7619
59 1Q3A NGH 4.84848
60 1KUK PCA LYS TRP 4.92611
61 4DR9 BB2 5.20833
62 2GN2 C5P 5.26316
63 5O7E 9NB 5.34351
64 1NME 159 5.43478
65 4WKI 3PW 5.53191
66 4QHP 32Q 5.55556
67 4AR8 IP8 GLY PRO ALA 5.58376
68 1KQR MNA 5.58659
69 3FXU TSU 5.90164
70 1RM8 BAT 5.91716
71 1FBL HTA 5.94595
72 4IN9 SER TRP PHE PRO 6.0241
73 5OLK DTP 6.04651
74 2HJ9 AI2 6.19469
75 2P3I MNA 6.21118
76 3AHO 3A2 6.48148
77 3E3U NVC 6.59898
78 2VWA PTY 6.93069
79 5L44 K26 6.94444
80 1MMQ RRS 7.05882
81 1G27 BB1 7.14286
82 4OVZ P85 7.27848
83 4OW0 S88 7.27848
84 3HBV ALA LYS ALA SER GLN ALA ALA 7.40741
85 1R55 097 7.47664
86 4TMN 0PK 7.59494
87 5JF2 SF7 7.84314
88 3RLF MAL 7.87037
89 5KK4 44E 8.33333
90 3KP6 SAL 8.60927
91 1LQY BB2 8.69565
92 1Q1Y BB2 8.90052
93 6G5J EM8 9.09091
94 5F74 AMP 9.18367
95 1ZED PNP 9.49074
96 3Q2H QHF 9.76431
97 2ZWS PLM 9.9537
98 5LWY OLB 10.2804
99 1RL4 BRR 10.6383
100 5XL4 SIA 10.7034
101 4UXU MLK 11.0092
102 4WZV E40 11.25
103 1WS1 BB2 11.5385
104 1R6N 434 12.3223
105 5V4R MGT 12.3457
106 1NU4 MLA 12.3711
107 6BMN PAP 12.8814
108 4XUB 43D 13.6752
109 2Y69 CHD 15
110 5M36 9SZ 15.7895
111 2TCL RO4 17.7515
112 1BWO LPC 18.8889
113 5Z84 CHD 19.1489
114 5W97 CHD 19.1489
115 5ZCO CHD 19.1489
116 3KO0 TFP 22.7723
117 5UGW GSH 24
118 4OGQ 7PH 29.4118
119 3D3X ARG ILE MET GLU NH2 49.6487
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