Receptor
PDB id Resolution Class Description Source Keywords
1NOW 2.2 Å EC: 3.2.1.52 HUMAN LYSOSOMAL BETA-HEXOSAMINIDASE ISOFORM B IN COMPLEX WIT 4S,5R)-2-ACETAMIDO-3,4-DIHYDROXY-5-HYDROXYMETHYL-PIPERIDINIC HLORIDE (GALNAC-ISOFAGOMINE) 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...
IFG A:557;
B:558;
Valid;
Valid;
none;
none;
submit data
204.224 C8 H16 N2 O4 CC(=O...
NAG NAG A:2;
B:4;
Part of Protein;
Part of Protein;
none;
none;
submit data
408.404 n/a O=C(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
1NOW 2.2 Å EC: 3.2.1.52 HUMAN LYSOSOMAL BETA-HEXOSAMINIDASE ISOFORM B IN COMPLEX WIT 4S,5R)-2-ACETAMIDO-3,4-DIHYDROXY-5-HYDROXYMETHYL-PIPERIDINIC HLORIDE (GALNAC-ISOFAGOMINE) 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 (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 1O7A - GDL C8 H13 N O6 CC(=O)N[C@....
2 1NOW - IFG 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 16 families.
1 1O7A - GDL C8 H13 N O6 CC(=O)N[C@....
2 1NOW - IFG 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 12 families.
1 1O7A - GDL C8 H13 N O6 CC(=O)N[C@....
2 1NOW - IFG C8 H16 N2 O4 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: IFG; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 IFG 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NOW; Ligand: IFG; Similar sites found: 126
This union binding pocket(no: 1) in the query (biounit: 1now.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.01803 0.41587 None
2 4R33 TRP 0.0003223 0.49313 1.19048
3 4R33 SAH 0.0003223 0.49313 1.19048
4 1Z42 HBA 0.005057 0.44885 1.47929
5 4NAO AKG 0.002258 0.42672 1.53374
6 3B8I OXL 0.01825 0.40724 1.74216
7 1EBG PAH 0.02701 0.40029 1.83486
8 4LWA Q13 0.004722 0.44666 1.92837
9 2PWY SAH 0.007773 0.41785 1.93798
10 2YVF FAD 0.00988 0.44695 1.96078
11 2YVF NAD 0.01019 0.44695 1.96078
12 3IHB TRS 0.007226 0.40891 1.97368
13 3TKA CTN 0.006209 0.42255 2.30548
14 3KJI ADP 0.00598 0.41174 2.3622
15 3Q9T FAY 0.007838 0.43539 2.36686
16 1PX8 XYP 0.001175 0.42469 2.4
17 3HZL 6PC 0.005012 0.42647 2.51889
18 2WQP WQP 0.005392 0.42944 2.5788
19 4N7U 2JA 0.003138 0.43607 2.63158
20 2VDJ HSE 0.004007 0.42312 2.65781
21 2CW6 3HG 0.008714 0.41511 2.68456
22 1Y1A GSH 0.001444 0.48423 2.73224
23 4O8A 2OP 0.001647 0.44928 2.76134
24 4RJK PYR 0.005338 0.41749 2.76134
25 3ZGE ASP 0.01057 0.40405 2.76134
26 3QCJ NX4 0.02649 0.40935 2.90323
27 1KTC NGA 0.001086 0.41505 2.96296
28 1I0Z OXM 0.01241 0.40784 3.003
29 4N02 FNR 0.006003 0.45242 3.08123
30 2J8Z NAP 0.008199 0.42407 3.10734
31 2PTZ PAH 0.004535 0.41682 3.24074
32 1ZFJ IMP 0.01773 0.42342 3.25866
33 2YD6 FLC 0.008813 0.41353 3.30189
34 9LDB OXM 0.01094 0.41831 3.31325
35 9LDT OXM 0.0119 0.41649 3.31325
36 1MZV AMP 0.0004848 0.41095 3.40426
37 4EXO PYR 0.00287 0.42966 3.42466
38 3VPD BUA 0.01765 0.42324 3.55872
39 2BZ1 TAU 0.0008844 0.48414 3.57143
40 2V7T SAH 0.04184 0.42778 3.67893
41 1O9U ADZ 0.002074 0.44455 3.71429
42 3MYU VIB 0.006584 0.41425 3.77907
43 3A8U PLP 0.01862 0.40261 3.78619
44 1XX4 BAM 0.01368 0.40582 3.83142
45 1GAD NAD 0.009896 0.41768 3.93939
46 1XHL NDP 0.01141 0.42131 4.0404
47 1OMZ UD2 0.01223 0.43107 4.09556
48 1PR9 NAP 0.01019 0.42472 4.09836
49 1Y7I SAL 0.001995 0.4039 4.10448
50 4F8L GAL 0.006233 0.43999 4.13793
51 3BLI ACO 0.01049 0.41053 4.1543
52 3UBW 6SP 0.0009155 0.49966 4.21456
53 1P9P SAH 0.01038 0.41072 4.21456
54 3PNL ADP 0.002472 0.43794 4.2654
55 4AZC NGW 0.0000004406 0.6273 4.29864
56 3R51 MMA 0.003818 0.43205 4.375
57 1XE7 GUN 0.008851 0.41479 4.4335
58 4G1V FAD 0.01504 0.40955 4.51128
59 4DVE BTN 0.001775 0.42656 4.54545
60 3E5P PPI 0.02844 0.41698 4.58221
61 1H16 DTL 0.01173 0.409 4.73373
62 1H16 PYR 0.009791 0.40557 4.73373
63 1TDF NAP 0.03694 0.42385 4.74684
64 1TDF FAD 0.0397 0.40908 4.74684
65 3MAG 3MA 0.001198 0.46586 4.88599
66 4WBD ADP 0.008119 0.40263 4.93097
67 3MCT 3MC 0.001657 0.40873 5.05051
68 4M51 BEZ 0.006119 0.4148 5.15223
69 4TMK T5A 0.003345 0.49165 5.16432
70 4W6Z ETF 0.01465 0.40442 5.18732
71 4B16 NAG 0.009963 0.42032 5.26316
72 1FDJ 2FP 0.000743 0.44492 5.50964
73 1WTC ACP 0.007797 0.4034 5.57276
74 1YOA FMN 0.01147 0.42617 5.66038
75 1Q3Q ANP 0.002459 0.47423 5.71992
76 3T2W BTN 0.0009525 0.40198 5.7377
77 1IYE PGU 0.01801 0.41108 5.82524
78 4GYW UDP 0.01031 0.42332 6.1144
79 4M5P MLA 0.002813 0.44753 6.14251
80 4M5P 23W 0.004957 0.41894 6.14251
81 4DXJ IPE 0.002413 0.41829 6.35359
82 4DXJ 0M9 0.00333 0.41528 6.35359
83 2QLX RM4 0.003134 0.42056 6.48148
84 2V5E SCR 0.006435 0.42974 6.5
85 1C1L GAL BGC 0.003991 0.41601 6.56934
86 1RY2 AMP 0.002869 0.4401 6.70611
87 3PAK MAN 0.01053 0.40235 6.75676
88 3L24 GOA 0.01781 0.40038 6.90335
89 2C4I BTN 0.004556 0.41674 7.01107
90 3BHO B4P 0.02116 0.40404 7.21154
91 1JGS SAL 0.02894 0.40506 7.24638
92 2DKH FAD 0.02334 0.40819 7.29783
93 2DKH 3HB 0.03984 0.40325 7.29783
94 1GU3 BGC BGC BGC BGC BGC 0.001533 0.40909 7.38255
95 2GDZ NAD 0.009376 0.42274 7.49064
96 1R37 NAD 0.01019 0.42585 7.4928
97 3S9K CIT 0.00101 0.50455 7.62712
98 1SS4 CIT 0.0004393 0.49244 7.84314
99 1SS4 GSH 0.006699 0.44849 7.84314
100 1KO0 LYS 0.002883 0.42957 8
101 1KO0 DLY 0.005013 0.41172 8
102 1ZED PNP 0.00471 0.41289 8.26446
103 3SCH TB6 0.002842 0.41559 8.58586
104 3CL5 SIO 0.006779 0.40603 9.01857
105 1H8P PC 0.00777 0.41746 9.17431
106 2Q97 ATP 0.008696 0.41409 9.30233
107 1V5F TPP 0.04419 0.44121 9.66469
108 1V5F FAD 0.04419 0.44121 9.66469
109 3SQG COM 0.003244 0.44447 10.0358
110 1YAG ATP 0.006415 0.42151 10.4
111 4BAS GNP 0.002979 0.43261 11.5578
112 2XI7 XI7 0.00998 0.42932 11.9565
113 1JAC AMG 0.0009137 0.47168 12.782
114 1FIQ SAL 0.004608 0.43924 12.7854
115 1FIQ FAD 0.01626 0.41651 12.7854
116 1FIQ MTE 0.0294 0.4002 12.7854
117 2AEB ABH 0.01123 0.42335 14.2857
118 1V7R CIT 0.01826 0.40723 15.5914
119 3U5S FAD 0.01298 0.40484 17.4603
120 1E7S NAP 0.009623 0.42468 21.4953
121 4A6F SEP 0.01758 0.40806 21.6667
122 4JAW GAL NGT 0.00003688 0.48486 23.4714
123 4JAW NGT GAL 0.00003971 0.4626 23.4714
124 1T0S BML 0.008349 0.4087 25.4545
125 3PMA SCR 0.002563 0.40162 37.931
126 4LSJ LSJ 0.003398 0.43013 46.1538
Pocket No.: 2; Query (leader) PDB : 1NOW; Ligand: IFG; Similar sites found: 58
This union binding pocket(no: 2) in the query (biounit: 1now.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2XUM OGA 0.006389 0.40392 1.14613
2 1Z44 NPO 0.02783 0.40867 1.47929
3 2ZWS PLM 0.02996 0.40697 1.57791
4 2BLE 5GP 0.02773 0.41993 1.90736
5 3E4O SIN 0.002257 0.40367 1.96721
6 2GWD GLU 0.002503 0.40038 2.00445
7 1RQH PYR 0.002209 0.43032 2.16963
8 3H22 B53 0.00125 0.40325 2.3569
9 1B55 4IP 0.0005132 0.40011 2.36686
10 1H9G COA MYR 0.003471 0.43229 2.46914
11 3GJB AKG 0.0006453 0.42182 2.50784
12 4QVH FLC 0.000767 0.49583 2.5641
13 2ZYF AKG 0.0003217 0.43288 2.6178
14 2C31 ADP 0.02866 0.42505 2.76134
15 2C31 TZD 0.02939 0.42505 2.76134
16 3O03 GCO 0.009697 0.41582 3.35306
17 4G10 GSH 0.002891 0.4193 3.39623
18 2W8Q SIN 0.007047 0.40827 3.5503
19 3VPD CIT 0.01613 0.41273 3.55872
20 1X54 4AD 0.009047 0.41142 3.68664
21 4M2K PLP 0.001934 0.40404 3.69458
22 1BTN I3P 0.01403 0.42651 3.77358
23 1KBJ FMN 0.00645 0.41922 3.8835
24 1H0C AOA 0.001488 0.43782 4.08163
25 1KC7 PPR 0.0104 0.40087 4.14201
26 1JN2 SFP 0.03924 0.40084 4.21941
27 3ZLM ANP 0.01042 0.40044 4.25532
28 3CBG 4FE 0.01374 0.41623 4.31034
29 3F81 STT 0.008071 0.41231 4.37158
30 1HEX NAD 0.01815 0.40258 4.63768
31 1ULE GLA GAL NAG 0.002472 0.42127 4.66667
32 4DQ2 BTX 0.005349 0.42701 4.87805
33 3QDW A2G 0.01899 0.40184 4.8951
34 1PEA ACM 0.00364 0.4281 4.93506
35 1NU4 MLA 0.03447 0.40373 5.15464
36 2YCJ C2F 0.00573 0.40497 5.16605
37 1H8G CHT 0.01154 0.4289 5.26316
38 2VKL MLT 0.002859 0.45032 5.55556
39 3DAG FEG 0.001733 0.44369 5.86592
40 1QB7 ADE 0.001075 0.40656 5.9322
41 2H6B 3C4 0.008611 0.41383 6
42 2D37 NAD 0.01156 0.41111 6.25
43 2D37 FMN 0.01075 0.41111 6.25
44 1YHM AHD 0.005492 0.40087 6.35359
45 4N7C AEF 0.009767 0.40206 6.81818
46 3WUD GLC GAL 0.001343 0.44783 7.35294
47 2F01 BTN 0.03504 0.41804 8.66142
48 2F01 BTQ 0.03735 0.41669 8.66142
49 3CL7 HYN 0.001998 0.43941 9.41558
50 3E6J DR2 0.02371 0.40066 9.60699
51 1P72 THM 0.003949 0.40109 9.88024
52 1UW1 ADP 0.002247 0.4166 10
53 2X2T GAL NGA 0.006649 0.42364 12.4183
54 2AZ3 CDP 0.003575 0.40277 12.8049
55 1I1Q TRP 0.001765 0.40597 13.0208
56 2W3L DRO 0.01486 0.40695 13.8889
57 2VQ5 LDP 0.008756 0.41794 16.9154
58 4COQ SAN 0.004554 0.41012 18.2186
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