Receptor
PDB id Resolution Class Description Source Keywords
2VC9 2.36 Å EC: 3.2.1.50 FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH 2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN CLOSTRIDIUM PERFRINGENS MUCOPOLYSACCHARIDOSIS 2-ACETAMIDO-1 2-DIDEOXYNOJIRMYCIN GH89 NAGLU SANFILIPPO DISEASE HYDROLASE ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY 89 GLYCOSIDE HYDROLASE
Ref.: STRUCTURAL AND MECHANISTIC INSIGHT INTO THE BASIS OF MUCOPOLYSACCHARIDOSIS IIIB. PROC.NATL.ACAD.SCI.USA V. 105 6560 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1912;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
GOL A:1910;
A:1911;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NOK A:1909;
Valid;
none;
Kd = 3.6 nM
204.224 C8 H16 N2 O4 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VC9 2.36 Å EC: 3.2.1.50 FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH 2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN CLOSTRIDIUM PERFRINGENS MUCOPOLYSACCHARIDOSIS 2-ACETAMIDO-1 2-DIDEOXYNOJIRMYCIN GH89 NAGLU SANFILIPPO DISEASE HYDROLASE ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY 89 GLYCOSIDE HYDROLASE
Ref.: STRUCTURAL AND MECHANISTIC INSIGHT INTO THE BASIS OF MUCOPOLYSACCHARIDOSIS IIIB. PROC.NATL.ACAD.SCI.USA V. 105 6560 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2VCA - NAG C8 H15 N O6 CC(=O)N[C@....
2 2VC9 Kd = 3.6 nM NOK C8 H16 N2 O4 CC(=O)N[C@....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2VCA - NAG C8 H15 N O6 CC(=O)N[C@....
2 2VC9 Kd = 3.6 nM NOK C8 H16 N2 O4 CC(=O)N[C@....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2VCA - NAG C8 H15 N O6 CC(=O)N[C@....
2 2VC9 Kd = 3.6 nM NOK C8 H16 N2 O4 CC(=O)N[C@....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NOK; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 NOK 1 1
2 DJN 1 1
3 1BW 0.632653 0.882353
4 HQ6 0.52 0.857143
5 2CZ 0.510638 0.836735
6 F34 0.510638 0.836735
7 LTM 0.403846 0.895833
Similar Ligands (3D)
Ligand no: 1; Ligand: NOK; Similar ligands found: 323
No: Ligand Similarity coefficient
1 NAG 0.9985
2 NDG 0.9780
3 GDL 0.9718
4 TNX 0.9689
5 NGW 0.9551
6 NGT 0.9511
7 BEU 0.9501
8 A2G 0.9445
9 BM3 0.9427
10 57O 0.9399
11 BNX 0.9389
12 IFG 0.9383
13 EPR 0.9370
14 ALX 0.9363
15 9H2 0.9363
16 NGA 0.9360
17 MQG 0.9354
18 GC2 0.9331
19 LOG 0.9306
20 86L 0.9303
21 SNG 0.9299
22 OQC 0.9295
23 K82 0.9281
24 3VX 0.9277
25 GC3 0.9270
26 NGO 0.9254
27 2F8 0.9230
28 8NX 0.9221
29 8NB 0.9205
30 3XR 0.9178
31 NHT 0.9170
32 GZQ 0.9166
33 GF4 0.9165
34 61M 0.9151
35 HHT 0.9149
36 ZZZ 0.9149
37 J6W 0.9145
38 IAC 0.9133
39 MAG 0.9128
40 3N1 0.9125
41 ST2 0.9118
42 12T 0.9113
43 9R5 0.9109
44 YTX 0.9106
45 BGN 0.9095
46 NLA 0.9089
47 GJP 0.9086
48 3C4 0.9084
49 CH8 0.9080
50 9KH 0.9080
51 GCU 0.9080
52 YI6 0.9080
53 BBK 0.9077
54 BDP 0.9074
55 NB1 0.9073
56 0FN 0.9070
57 4HP 0.9062
58 PMP 0.9061
59 PHE 0.9061
60 54Z 0.9055
61 4RU 0.9052
62 6FZ 0.9045
63 LIP 0.9035
64 NSG 0.9033
65 2FX 0.9031
66 NFM 0.9028
67 NOJ 0.9019
68 5FN 0.9018
69 S0G 0.9012
70 TYL 0.9001
71 ZPF 0.9000
72 JTH 0.9000
73 5OF 0.8998
74 MS9 0.8997
75 PLP 0.8995
76 42J 0.8993
77 MJ5 0.8985
78 I3E 0.8985
79 BPY 0.8985
80 27B 0.8983
81 TYE 0.8980
82 PQZ 0.8980
83 DHY 0.8973
84 5OO 0.8972
85 MUR 0.8972
86 2BX 0.8972
87 LDP 0.8972
88 3DM 0.8970
89 F5C 0.8960
90 ICB 0.8955
91 MD6 0.8954
92 AAN 0.8954
93 CFA 0.8954
94 15N 0.8953
95 4AA 0.8952
96 IFL 0.8948
97 LCN 0.8946
98 TSR 0.8944
99 ST3 0.8943
100 S8A 0.8943
101 92P 0.8943
102 GLC 0.8942
103 9BF 0.8940
104 GNL 0.8938
105 BGC 0.8936
106 ARP 0.8934
107 14W 0.8934
108 NOY 0.8932
109 1FD 0.8930
110 QMS 0.8929
111 8WO 0.8928
112 EE8 0.8926
113 G6P 0.8922
114 EYV 0.8921
115 AES 0.8917
116 K3Q 0.8913
117 BCU 0.8908
118 AMH 0.8908
119 SYE 0.8908
120 APS 0.8901
121 0JD 0.8899
122 4NS 0.8897
123 ASO 0.8895
124 PFL 0.8894
125 IOP 0.8889
126 FPL 0.8889
127 2K8 0.8888
128 PA1 0.8885
129 6HP 0.8884
130 657 0.8883
131 MAJ 0.8883
132 N4E 0.8876
133 H4B 0.8876
134 UA5 0.8875
135 MNM 0.8875
136 S24 0.8874
137 9ZE 0.8872
138 A7N 0.8872
139 PYU 0.8871
140 8ZE 0.8870
141 G2F 0.8862
142 M3Q 0.8859
143 R9Y 0.8859
144 0LH 0.8859
145 AEG 0.8857
146 IOS 0.8857
147 ODO 0.8854
148 TMG 0.8854
149 DVQ 0.8846
150 C53 0.8840
151 MQB 0.8839
152 2BG 0.8839
153 K4V 0.8835
154 LGC 0.8834
155 88L 0.8832
156 N3W 0.8832
157 H7Y 0.8831
158 CLU 0.8829
159 VXX 0.8826
160 F69 0.8825
161 4A5 0.8825
162 JF1 0.8824
163 NVU 0.8824
164 GLO 0.8823
165 LNR 0.8823
166 2CL 0.8822
167 R9S 0.8819
168 GCS 0.8817
169 948 0.8816
170 NBG 0.8816
171 RH1 0.8815
172 GLP 0.8814
173 AX3 0.8813
174 GAL 0.8811
175 YRL 0.8810
176 OKM 0.8809
177 VOH 0.8806
178 94B 0.8806
179 MP5 0.8803
180 327 0.8802
181 EVA 0.8802
182 AEF 0.8796
183 AEH 0.8796
184 KP6 0.8793
185 AVO 0.8791
186 MMS 0.8791
187 8W9 0.8791
188 YX1 0.8788
189 STZ 0.8788
190 ALE 0.8788
191 S7G 0.8786
192 8U3 0.8785
193 GWM 0.8783
194 MPP 0.8782
195 SOE 0.8782
196 HA5 0.8779
197 6DP 0.8778
198 2UB 0.8776
199 HNT 0.8774
200 X1P 0.8773
201 PPN 0.8771
202 NPA 0.8771
203 OMD 0.8771
204 GLF 0.8770
205 Z13 0.8770
206 MS0 0.8769
207 N2I 0.8769
208 G3F 0.8767
209 RVE 0.8763
210 MR1 0.8762
211 I2E 0.8760
212 SHG 0.8759
213 F1X 0.8753
214 GCB 0.8752
215 AFR 0.8751
216 TAG 0.8749
217 PLR 0.8748
218 L21 0.8748
219 GSY 0.8748
220 FTV 0.8747
221 PXM 0.8746
222 4R1 0.8746
223 PW1 0.8746
224 3LJ 0.8744
225 ZON 0.8740
226 HDL 0.8739
227 G1P 0.8737
228 STT 0.8737
229 R1P 0.8733
230 2AL 0.8731
231 CN0 0.8730
232 FER 0.8728
233 BG6 0.8726
234 2A9 0.8724
235 A5P 0.8723
236 GLA 0.8721
237 MNP 0.8717
238 8MP 0.8716
239 EMZ 0.8716
240 IPD 0.8715
241 1CY 0.8713
242 DAH 0.8712
243 SBK 0.8712
244 HWD 0.8712
245 FRU 0.8710
246 DEE 0.8709
247 3MG 0.8708
248 L1Q 0.8707
249 FWD 0.8707
250 0FK 0.8707
251 HDH 0.8705
252 2FY 0.8703
253 2QC 0.8701
254 2HC 0.8700
255 EOL 0.8699
256 TSS 0.8698
257 ASC 0.8697
258 4FA 0.8697
259 ZXD 0.8694
260 2GS 0.8694
261 PRZ 0.8694
262 505 0.8693
263 CS2 0.8693
264 TZM 0.8692
265 ABF 0.8691
266 HJ7 0.8691
267 LYL 0.8690
268 MTL 0.8689
269 HHH 0.8686
270 ISD 0.8681
271 DTR 0.8675
272 ICT 0.8672
273 L46 0.8672
274 X0W 0.8669
275 A6P 0.8666
276 GCV 0.8655
277 CIT 0.8655
278 PXP 0.8651
279 X09 0.8648
280 HPT 0.8648
281 FLC 0.8647
282 97T 0.8646
283 CP7 0.8645
284 BMA 0.8643
285 SOR 0.8639
286 FUD 0.8639
287 P7Y 0.8638
288 E1P 0.8636
289 HQ9 0.8635
290 F6P 0.8634
291 7QD 0.8632
292 3RI 0.8628
293 RBJ 0.8626
294 4JE 0.8618
295 293 0.8618
296 BL0 0.8613
297 OA3 0.8611
298 5SP 0.8609
299 0QW 0.8606
300 2O8 0.8599
301 GXY 0.8598
302 SQV 0.8587
303 S3C 0.8587
304 CTS 0.8585
305 7MX 0.8584
306 3TC 0.8583
307 HSX 0.8580
308 5WZ 0.8575
309 RKN 0.8573
310 BY5 0.8570
311 SDF 0.8569
312 6Q3 0.8567
313 TLM 0.8567
314 KDG 0.8567
315 A3M 0.8564
316 DEZ 0.8563
317 ZYX 0.8560
318 1HN 0.8555
319 3W6 0.8551
320 3W3 0.8551
321 EN1 0.8533
322 ZB1 0.8515
323 TLG 0.8509
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VC9; Ligand: NOK; 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: 2vc9.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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