Receptor
PDB id Resolution Class Description Source Keywords
1NP0 2.5 Å EC: 3.2.1.52 HUMAN LYSOSOMAL BETA-HEXOSAMINIDASE ISOFORM B IN COMPLEX WIT INTERMEDIATE ANALOGUE NAG-THIAZOLINE HOMO SAPIENS (BETA/ALPHA)8-BARREL HOMODIMER FAMILY 20 GLYCOSIDASE HYDR
Ref.: CRYSTAL STRUCTURE OF HUMAN BETA-HEXOSAMINIDASE B: UNDERSTANDING THE MOLECULAR BASIS OF SANDHOFF AND T DISEASE J.MOL.BIOL. V. 327 1093 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:558;
A:559;
B:559;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NAG NAG A:2;
B:4;
Part of Protein;
Part of Protein;
none;
none;
submit data
408.404 n/a O=C(N...
NGT A:557;
B:558;
Valid;
Valid;
none;
none;
submit data
219.258 C8 H13 N O4 S CC1=N...
SO4 B:557;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1NP0 2.5 Å EC: 3.2.1.52 HUMAN LYSOSOMAL BETA-HEXOSAMINIDASE ISOFORM B IN COMPLEX WIT INTERMEDIATE ANALOGUE NAG-THIAZOLINE HOMO SAPIENS (BETA/ALPHA)8-BARREL HOMODIMER FAMILY 20 GLYCOSIDASE HYDR
Ref.: CRYSTAL STRUCTURE OF HUMAN BETA-HEXOSAMINIDASE B: UNDERSTANDING THE MOLECULAR BASIS OF SANDHOFF AND T DISEASE J.MOL.BIOL. V. 327 1093 2003
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 1NP0 - NGT C8 H13 N O4 S CC1=N[C@@H....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 1NP0 - NGT C8 H13 N O4 S CC1=N[C@@H....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 1NP0 - NGT C8 H13 N O4 S CC1=N[C@@H....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NGT; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 NGT 1 1
2 GNL 1 1
3 NHT 0.54717 0.833333
4 NB1 0.537037 0.918367
5 NGT GAL 0.492063 0.9
6 GAL NGT 0.492063 0.9
7 NGT NAG 0.464789 0.775862
8 SN5 NGT 0.464789 0.818182
9 SN5 SN5 NGT 0.428571 0.818182
10 NAG NAG NGT 0.428571 0.762712
11 BMA NGT MAN MAN 0.407407 0.9
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NP0; Ligand: NGT; Similar sites found: 209
This union binding pocket(no: 1) in the query (biounit: 1np0.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UXG FUM 0.01496 0.42746 2.48963
2 1UXG NAD 0.01496 0.42746 2.48963
3 2H6B 3C4 0.03735 0.41986 2.48963
4 1I9G SAM 0.04686 0.40919 2.90456
5 2HW1 ANP 0.01625 0.40567 2.90456
6 1A69 FMB 0.02275 0.43465 2.94118
7 1H9G COA MYR 0.00482 0.43752 3.15789
8 2FMD MAN MAN 0.01216 0.40963 3.15789
9 1GVF PGH 0.005596 0.40635 3.15789
10 2ALG HP6 0.006732 0.42292 3.26087
11 2ALG DAO 0.006732 0.42292 3.26087
12 1NW5 SAM 0.0144 0.40634 3.3195
13 4R33 TRP 0.000468 0.49323 3.68421
14 4R33 SAH 0.000468 0.49323 3.68421
15 1QF5 RPL 0.03343 0.41804 3.68421
16 1QF5 GDP 0.03343 0.41804 3.68421
17 1Z42 HBA 0.003439 0.45498 3.73444
18 1UZN NAP 0.01031 0.4071 3.73444
19 3CQD ATP 0.0233 0.41719 4.14938
20 5YAS FAC 0.006618 0.40865 4.56432
21 1YS4 NAP 0.02123 0.402 4.56432
22 2YBQ UP2 0.0139 0.42697 4.73684
23 1SOW NAD 0.01821 0.41704 4.73684
24 2YBQ SAH 0.0133 0.40789 4.73684
25 4EXO PYR 0.003592 0.42192 4.79452
26 1Y1A GSH 0.001338 0.4823 5.17241
27 1DSS NAD 0.009116 0.42332 5.17241
28 4KQI NIO 0.02132 0.41264 5.17241
29 4KQI RBZ 0.02132 0.41264 5.17241
30 3HY3 10F 0.01489 0.41056 5.17241
31 3D3W NAP 0.007065 0.43521 5.26316
32 2CSN CKI 0.01007 0.42133 5.26316
33 2XK9 XK9 0.01771 0.41982 5.26316
34 1P72 THM 0.001503 0.40139 5.26316
35 1QB7 ADE 0.0005188 0.45598 5.50847
36 2B82 ADN 0.001901 0.4476 5.6872
37 1KOL NAD 0.01574 0.42438 5.78947
38 1R18 SAH 0.01417 0.40998 5.78947
39 3H22 B53 0.0009408 0.44493 5.80913
40 3IL6 B83 0.01608 0.40418 6.22407
41 3R51 MMA 0.003207 0.43225 6.25
42 4U36 TNR 0.00797 0.4245 6.25
43 1WVG CXY 0.005138 0.42994 6.31579
44 1WVG APR 0.01736 0.41043 6.31579
45 1OGZ EQU 0.003783 0.42159 6.4
46 3IB8 AMP 0.00439 0.42116 6.89655
47 1C1L GAL BGC 0.003376 0.4158 6.89655
48 3SVL FMN 0.001085 0.45227 7.36842
49 3Q9T FAY 0.01289 0.43057 7.36842
50 1GSA ADP 0.003116 0.43975 7.46888
51 4TMK T5A 0.00562 0.44112 7.51174
52 1SBZ FMN 0.03644 0.40271 7.61421
53 1SS4 GSH 0.00009097 0.54062 7.84314
54 4RNX FMN 0.006617 0.42237 7.88382
55 3VPD ANP 0.009002 0.41724 7.89474
56 1MG1 MAL 0.02036 0.40283 7.89474
57 1VDC FAD 0.008317 0.44797 8.29876
58 2NLI FMN 0.02842 0.42719 8.29876
59 2NLI LAC 0.03996 0.42092 8.29876
60 2DTX BMA 0.01752 0.4251 8.42105
61 3KJI ADP 0.004704 0.42207 8.42105
62 2OI2 DP6 0.01041 0.40258 8.42105
63 4P3H 25G 0.005827 0.45296 8.62069
64 2J7T 274 0.003094 0.44929 8.62069
65 1T57 FMN 0.004524 0.43244 8.62069
66 1JUV NDP 0.009373 0.42419 8.62069
67 1OTH PAO 0.0151 0.42089 8.62069
68 2PYU IMP 0.002226 0.42 8.62069
69 1XE7 GUN 0.006343 0.4184 8.62069
70 4IOK ADP 0.01626 0.41312 8.62069
71 5T0A A3P 0.006111 0.41138 8.62069
72 3N5O GSH 0.01104 0.4097 8.62069
73 4F2Q QUS 0.008081 0.40961 8.62069
74 1R27 MGD 0.03281 0.40903 8.62069
75 2J0W ADP 0.01059 0.40861 8.62069
76 3TO7 COA 0.04638 0.40359 8.62069
77 4C0X AQN 0.03422 0.4029 8.62069
78 1BGQ RDC 0.006519 0.43147 8.88889
79 1YOE RIB 0.00442 0.41351 8.94737
80 2D37 NAD 0.01609 0.41467 9.09091
81 2D37 FMN 0.01505 0.41467 9.09091
82 3IOI 1GW 0.006743 0.4374 9.12863
83 2F01 BTN 0.01398 0.44727 9.44882
84 3S2Y FMN 0.006231 0.42076 9.47368
85 1D3V ABH 0.02598 0.40233 9.47368
86 2HVW DCP 0.004619 0.42019 9.78261
87 2HVW DDN 0.009046 0.40747 9.78261
88 1JIL 485 0.01296 0.40839 9.95851
89 2PT9 S4M 0.02109 0.40653 9.95851
90 2PT9 2MH 0.04452 0.40062 9.95851
91 2HXT EHM 0.0002593 0.47456 10
92 2C4I BTN 0.003686 0.42671 10
93 4DXJ 0M9 0.007169 0.40716 10
94 3TA2 AKG 0.02846 0.40434 10.1695
95 1R37 NAD 0.01066 0.43033 10.3448
96 2VJJ RAM GLC GAL NAG NAG GLC 0.02981 0.42165 10.3448
97 3K56 IS3 0.004513 0.42064 10.3448
98 3DDC GNP 0.0163 0.41169 10.3448
99 2HGS ADP 0.0139 0.41037 10.3448
100 1XVV CCQ 0.03566 0.41008 10.3448
101 1LCP PLU 0.02069 0.40691 10.3448
102 4G1V FAD 0.02271 0.40639 10.3448
103 3RFV 15L 0.02582 0.40379 10.3448
104 1R37 ETX 0.005476 0.40047 10.3448
105 3RFV NAI 0.0331 0.40003 10.3448
106 4M5P MLA 0.003582 0.43899 10.3734
107 4LNL 2BK 0.0005443 0.46308 10.5263
108 4LNL 2BO 0.0005443 0.46308 10.5263
109 3VKX T3 0.002903 0.43841 10.5263
110 4C1K PEP 0.001936 0.42573 10.5263
111 1Q3Q ANP 0.02987 0.42478 10.7884
112 4DL8 UMP AF3 PO4 0.01564 0.40472 10.7884
113 1TU3 GNP 0.005757 0.43248 11.1111
114 3ZY6 GFB 0.01696 0.40483 11.2033
115 4PO2 ASN ARG LEU LEU LEU THR GLY 0.01216 0.41611 11.4894
116 3MAG 3MA 0.00668 0.42572 11.6183
117 3MCT 3MC 0.001052 0.40852 11.6183
118 3ZLM ANP 0.0009061 0.45792 12.069
119 1OIK C26 0.001386 0.44532 12.069
120 1XOC VAL ASP SER LYS ASN THR SER SER TRP 0.008556 0.44112 12.069
121 4KCF AKM 0.004032 0.43639 12.069
122 2BZ1 TAU 0.008087 0.43091 12.069
123 1L1Q 9DA 0.005592 0.42474 12.069
124 4NTD FAD 0.0193 0.42211 12.069
125 1PL6 NAD 0.007912 0.42146 12.069
126 3E5P PPI 0.02198 0.41817 12.069
127 4F8L GAL 0.02001 0.4105 12.069
128 3V1U NAD 0.02052 0.40708 12.069
129 3PY5 AMP 0.002324 0.43549 12.1053
130 2X2T GAL NGA 0.004238 0.4266 12.4183
131 4LXH C1E 0.01292 0.40477 13.278
132 1JAC AMG 0.0007903 0.47115 13.5338
133 2NZU BG6 0.007108 0.40197 13.6364
134 3FS8 ACO 0.02296 0.44121 13.6842
135 4O1M NAD 0.009017 0.42898 13.6842
136 2CKM AA7 0.02495 0.41945 13.6842
137 1JGS SAL 0.00416 0.44583 13.7681
138 2GSD NAD 0.004806 0.44789 13.7931
139 4DVE BTN 0.001291 0.43905 13.7931
140 1FDJ 2FP 0.001731 0.43624 13.7931
141 1GAD NAD 0.007482 0.42871 13.7931
142 4LWA Q13 0.0187 0.42373 13.7931
143 4HZX G39 0.01904 0.42335 13.7931
144 2C7G FAD 0.03979 0.41912 13.7931
145 2C7G ODP 0.03862 0.41912 13.7931
146 8CAT NDP 0.008442 0.4185 13.7931
147 2V5E SCR 0.009881 0.41736 13.7931
148 4AQL TXC 0.008353 0.41316 13.7931
149 1XHL NDP 0.0249 0.41059 13.7931
150 4GYW UDP 0.0263 0.40946 13.7931
151 2QDT I38 0.009507 0.40866 13.7931
152 1MZV AMP 0.0003521 0.40829 13.7931
153 1UBY DMA 0.01453 0.40251 13.7931
154 1A8R GTP 0.01555 0.40484 14.0271
155 1RY2 AMP 0.008849 0.42391 14.1079
156 1XNK XS2 0.001308 0.44642 14.2105
157 3L24 GOA 0.005607 0.42091 14.5228
158 2OYS FMN 0.01932 0.40227 14.5228
159 4BMO FMN 0.01153 0.41862 14.7368
160 1E7S NAP 0.01785 0.41745 14.7368
161 1F8F NAD 0.02605 0.42778 14.9378
162 3CL7 HYN 0.009595 0.42081 15.2632
163 3LIH RAF 0.009534 0.41254 15.5172
164 1ZED PNP 0.006012 0.40505 15.5172
165 2VKL MLT 0.004051 0.43638 15.5556
166 4PLG NAI 0.01171 0.43157 16.1826
167 4PLG OXM 0.01171 0.43157 16.1826
168 1LTH NAD 0.01565 0.44162 17.2414
169 3H86 AP5 0.01573 0.4331 17.2414
170 2AMV BIN 0.02053 0.4301 17.2414
171 4IVG ANP 0.03827 0.41657 17.2414
172 4LFL TG6 0.007309 0.4068 17.2414
173 2DKH 3HB 0.02721 0.41582 17.3684
174 4NES UDP 0.01195 0.40628 17.8423
175 3WO0 ALA 0.004145 0.45208 18.4211
176 3WO0 ADP 0.004145 0.45208 18.4211
177 1R89 CTP 0.01044 0.40688 18.9474
178 1NVU GTP 0.006617 0.4576 18.9655
179 1C0I FAD 0.01475 0.43405 18.9655
180 1C0I BE2 0.01475 0.43405 18.9655
181 1OFH ADP 0.008635 0.4244 18.9655
182 2JE7 XMM 0.009795 0.42331 19.4737
183 3GE7 AFQ 0.02345 0.41293 20.5263
184 3GEG NAD 0.02247 0.40791 20.5263
185 1TDF NAP 0.01625 0.44684 20.6897
186 3FED BIX 0.003361 0.43062 20.6897
187 1OMZ UD2 0.02015 0.42573 20.6897
188 3TKA CTN 0.005031 0.42509 20.6897
189 3QQA TCH 0.007815 0.4217 20.6897
190 1TDF FAD 0.03187 0.41831 20.6897
191 1P9P SAH 0.01617 0.40738 20.6897
192 4BCS BTN 0.0103 0.40713 21.6
193 1TUV VK3 0.01395 0.40235 22.4138
194 2GJ3 FAD 0.01627 0.40725 23.3333
195 2XVE FAD 0.003916 0.47334 24.1379
196 1IYE PGU 0.00276 0.45434 24.1379
197 1FIQ SAL 0.003497 0.45081 24.1379
198 1FIQ MTE 0.02107 0.4117 24.1379
199 1ZGA SAH 0.007594 0.41079 24.1379
200 4O8A 2OP 0.009255 0.41071 24.1379
201 1TIW TFB 0.03667 0.40858 24.1379
202 1TIW FAD 0.03667 0.40858 24.1379
203 2Q97 ATP 0.004468 0.43268 24.8062
204 4INB 1F6 0.005568 0.42482 25.8621
205 2PWY SAH 0.01163 0.41546 25.8621
206 3A8U PLP 0.003352 0.4126 29.3103
207 4ARF IP8 GLY PRO ALA 0.004636 0.42235 32.7586
208 3PMA SCR 0.001625 0.40137 37.931
209 4LSJ LSJ 0.01918 0.4024 46.1538
Pocket No.: 2; Query (leader) PDB : 1NP0; Ligand: NGT; Similar sites found: 64
This union binding pocket(no: 2) in the query (biounit: 1np0.bio3) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1VJT NAD 0.002167 0.44313 3.15789
2 1WGC SIA GAL BGC 0.01559 0.4076 3.50877
3 2BLE 5GP 0.03203 0.42583 3.68421
4 1Z44 NPO 0.001447 0.4695 3.73444
5 1XMV ADP 0.02038 0.43101 4.14938
6 3SCH TB6 0.005254 0.40121 4.73684
7 1OWB NAD 0.02534 0.40852 5.17241
8 1PR9 NAP 0.02113 0.41509 5.26316
9 1B9I PXG 0.005079 0.43184 5.39419
10 4TSK NDP 0.04076 0.41923 5.39419
11 4N02 FNR 0.02411 0.42807 6.31579
12 1FP1 SAH 0.01354 0.4019 6.31579
13 1NN5 2DT 0.0113 0.42439 6.89655
14 1NN5 ANP 0.0113 0.42439 6.89655
15 1V2G OCA 0.009698 0.40391 6.89655
16 3BHO B4P 0.006973 0.4248 7.21154
17 3BLI ACO 0.006436 0.42552 7.36842
18 3ZRR PXG 0.01696 0.40314 7.36842
19 4EKV BTN 0.01413 0.42339 7.54717
20 2BGM NAJ 0.01927 0.43572 7.88382
21 2IUW AKG 0.004535 0.41303 8.40336
22 1ZFJ IMP 0.0418 0.41009 8.42105
23 3R35 4CO 0.01497 0.41988 8.60927
24 1X54 4AD 0.01153 0.41715 8.62069
25 9LDT OXM 0.01545 0.4078 8.62069
26 3JDW ORN 0.01328 0.40227 8.62069
27 3O2K DST 0.001366 0.402 8.62069
28 3PNL ADP 0.02199 0.4013 8.62069
29 3TXO 07U 0.01291 0.40072 8.94737
30 2HGZ PBF 0.001483 0.45783 10.3448
31 3CBG SAH 0.003764 0.42845 10.3448
32 2GDZ NAD 0.01348 0.42081 10.5263
33 3SQG COM 0.00392 0.43708 12.069
34 1PL6 572 0.01267 0.42564 12.069
35 1PX8 XYP 0.001832 0.40957 12.069
36 4W6Z ETF 0.0148 0.40114 12.069
37 2YGN PCF 0.02055 0.41098 12.1795
38 2W3L DRO 0.01427 0.40188 12.5
39 1T8U UAP SGN IDS SGN 0.03174 0.41164 13.1579
40 3PJU C2E 0.02113 0.40784 13.1579
41 4CMF PXG 0.01666 0.43462 14.2105
42 1V35 NAI 0.02241 0.42173 14.2105
43 3EM1 TYD 0.002556 0.44622 14.3836
44 1T26 NAI 0.01495 0.45767 15.5172
45 1T26 GBD 0.01495 0.45767 15.5172
46 3MBG FAD 0.0231 0.40469 15.8273
47 1I2B USQ 0.0163 0.43801 17.2414
48 1I2B NAD 0.0163 0.43801 17.2414
49 1I2B UPG 0.0163 0.43801 17.2414
50 3UR0 SVR 0.01984 0.4269 17.2414
51 2EFJ SAH 0.008537 0.41274 17.2414
52 3ZS7 ATP 0.01894 0.40426 17.2414
53 4NES UD1 0.01285 0.40675 17.8423
54 3C1O NAP 0.004651 0.43519 18.9655
55 1V7R CIT 0.0119 0.41339 18.9655
56 1KWK GAL 0.006082 0.42122 22.4138
57 3DAG FEG 0.003571 0.442 24.0664
58 2X61 CH 0.004381 0.45415 24.1379
59 2X61 NGA GAL SIA 0.02541 0.42966 24.1379
60 1FIQ FAD 0.01886 0.41853 24.1379
61 3GWT 066 0.03322 0.40352 24.1379
62 1ZGA HMK 0.01158 0.40057 24.1379
63 1Y13 BIO 0.01048 0.40008 24.1379
64 3O03 NAP 0.001556 0.46013 29.3103
Pocket No.: 3; Query (leader) PDB : 1NP0; Ligand: NGT; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1np0.bio3) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1NP0; Ligand: NGT; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1np0.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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