Receptor
PDB id Resolution Class Description Source Keywords
2xm1 2 Å EC: 3.2.1.52 BTGH84 IN COMPLEX WITH N-ACETYL GLUCONOLACTAM BACTEROIDES THETAIOTAOMICRON VPI-5482 GLYCOSIDASE HYDROLASE INHIBITOR
Ref.: INHIBITION OF A BACTERIAL O-GLCNACASE HOMOLOGUE BY AND LACTAM DERIVATIVES: STRUCTURAL, KINETIC AND THERMODYNAMIC ANALYSES. AMINO ACIDS V. 40 829 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1716;
A:1718;
B:1717;
B:1718;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
LTM A:1717;
B:1716;
 Valid;
Valid;
 none;
none;
 Kd = 8.5 uM
218.207 C8 H14 N2 O5 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5ABH 1.95 Å EC: 3.2.1.52 STRUCTURE OF GH84 WITH LIGAND BACTEROIDES THETAIOTAOMICRON HYDROLASE TIM-BARREL INHIBITOR
Ref.: A CONVENIENT APPROACH TO STEREOISOMERIC IMINOCYCLIT GENERATION OF POTENT BRAIN-PERMEABLE OGA INHIBITORS ANGEW.CHEM.INT.ED.ENGL. V. 54 15429 2015
Members (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 2XJ7 Kd = 246 nM GC2 C10 H18 N2 O4 CC(=O)N[C@....
2 2WZH - NGO C8 H14 N O5 CC1=[NH+][....
3 4AIU - GC3 C8 H13 N O6 C([C@@H]1[....
4 2VVS Ki = 46 nM OAN C15 H19 N3 O7 CC(=O)N[C@....
5 2W66 Ki = 89 uM HQ6 C9 H18 N2 O5 CC(=O)N[C@....
6 2X0H - 14T C14 H15 F4 N O6 c1cc(c(cc1....
7 5ABG Ki = 9 nM V0N C17 H25 F N2 O4 CNC(=O)C[C....
8 4AIS - GOA C2 H4 O3 C(C(=O)O)O
9 2XM1 Kd = 8.5 uM LTM C8 H14 N2 O5 CC(=O)N[C@....
10 2W4X Kd = 14 uM STZ C8 H15 N3 O7 CN(C(=O)N[....
11 4UR9 Kd = 3.1 mM BK9 C10 H10 N2 O CCOc1c2ccc....
12 2WCA - NP6 C17 H23 N3 O7 CCCC(=O)N[....
13 2VVN - NHT C9 H16 N2 O4 S CCNC1=N[C@....
14 5ABE Ki = 890 uM XQO C13 H26 N2 O4 CCCCCN1[C@....
15 2J4G Ki = 0.25 uM NB1 C10 H17 N O4 S CCCC1=N[C@....
16 5MI7 - OAN C15 H19 N3 O7 CC(=O)N[C@....
17 5MI5 - OAN C15 H19 N3 O7 CC(=O)N[C@....
18 2WZI - 5FN C8 H12 F N O5 CC1=N[C@@H....
19 2JIW - BEU C9 H16 N2 O4 CC(=O)N[C@....
20 2W67 Ki = 11 uM F34 C8 H16 N2 O4 CC(=O)N[C@....
21 5ABH Ki = 1.7 nM YWN C13 H26 N2 O4 CCCCCN1[C@....
22 2XM2 Ki = 24 uM LOG C8 H14 N2 O6 CC(=O)N[C@....
23 5MI6 - NHT C9 H16 N2 O4 S CCNC1=N[C@....
24 2J47 Ki = 3.9 uM GDV C17 H21 N4 O5 CC(=O)N[C@....
70% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 2XJ7 Kd = 246 nM GC2 C10 H18 N2 O4 CC(=O)N[C@....
2 2WZH - NGO C8 H14 N O5 CC1=[NH+][....
3 4AIU - GC3 C8 H13 N O6 C([C@@H]1[....
4 2VVS Ki = 46 nM OAN C15 H19 N3 O7 CC(=O)N[C@....
5 2W66 Ki = 89 uM HQ6 C9 H18 N2 O5 CC(=O)N[C@....
6 2X0H - 14T C14 H15 F4 N O6 c1cc(c(cc1....
7 5ABG Ki = 9 nM V0N C17 H25 F N2 O4 CNC(=O)C[C....
8 4AIS - GOA C2 H4 O3 C(C(=O)O)O
9 2XM1 Kd = 8.5 uM LTM C8 H14 N2 O5 CC(=O)N[C@....
10 2W4X Kd = 14 uM STZ C8 H15 N3 O7 CN(C(=O)N[....
11 4UR9 Kd = 3.1 mM BK9 C10 H10 N2 O CCOc1c2ccc....
12 2WCA - NP6 C17 H23 N3 O7 CCCC(=O)N[....
13 2VVN - NHT C9 H16 N2 O4 S CCNC1=N[C@....
14 5ABE Ki = 890 uM XQO C13 H26 N2 O4 CCCCCN1[C@....
15 2J4G Ki = 0.25 uM NB1 C10 H17 N O4 S CCCC1=N[C@....
16 5MI7 - OAN C15 H19 N3 O7 CC(=O)N[C@....
17 5MI5 - OAN C15 H19 N3 O7 CC(=O)N[C@....
18 2WZI - 5FN C8 H12 F N O5 CC1=N[C@@H....
19 2JIW - BEU C9 H16 N2 O4 CC(=O)N[C@....
20 2W67 Ki = 11 uM F34 C8 H16 N2 O4 CC(=O)N[C@....
21 5ABH Ki = 1.7 nM YWN C13 H26 N2 O4 CCCCCN1[C@....
22 2XM2 Ki = 24 uM LOG C8 H14 N2 O6 CC(=O)N[C@....
23 5MI6 - NHT C9 H16 N2 O4 S CCNC1=N[C@....
24 2J47 Ki = 3.9 uM GDV C17 H21 N4 O5 CC(=O)N[C@....
50% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 2XJ7 Kd = 246 nM GC2 C10 H18 N2 O4 CC(=O)N[C@....
2 2WZH - NGO C8 H14 N O5 CC1=[NH+][....
3 4AIU - GC3 C8 H13 N O6 C([C@@H]1[....
4 2VVS Ki = 46 nM OAN C15 H19 N3 O7 CC(=O)N[C@....
5 2W66 Ki = 89 uM HQ6 C9 H18 N2 O5 CC(=O)N[C@....
6 2X0H - 14T C14 H15 F4 N O6 c1cc(c(cc1....
7 5ABG Ki = 9 nM V0N C17 H25 F N2 O4 CNC(=O)C[C....
8 4AIS - GOA C2 H4 O3 C(C(=O)O)O
9 2XM1 Kd = 8.5 uM LTM C8 H14 N2 O5 CC(=O)N[C@....
10 2W4X Kd = 14 uM STZ C8 H15 N3 O7 CN(C(=O)N[....
11 4UR9 Kd = 3.1 mM BK9 C10 H10 N2 O CCOc1c2ccc....
12 2WCA - NP6 C17 H23 N3 O7 CCCC(=O)N[....
13 2VVN - NHT C9 H16 N2 O4 S CCNC1=N[C@....
14 5ABE Ki = 890 uM XQO C13 H26 N2 O4 CCCCCN1[C@....
15 2J4G Ki = 0.25 uM NB1 C10 H17 N O4 S CCCC1=N[C@....
16 5MI7 - OAN C15 H19 N3 O7 CC(=O)N[C@....
17 5MI5 - OAN C15 H19 N3 O7 CC(=O)N[C@....
18 2WZI - 5FN C8 H12 F N O5 CC1=N[C@@H....
19 2JIW - BEU C9 H16 N2 O4 CC(=O)N[C@....
20 2W67 Ki = 11 uM F34 C8 H16 N2 O4 CC(=O)N[C@....
21 5ABH Ki = 1.7 nM YWN C13 H26 N2 O4 CCCCCN1[C@....
22 2XM2 Ki = 24 uM LOG C8 H14 N2 O6 CC(=O)N[C@....
23 5MI6 - NHT C9 H16 N2 O4 S CCNC1=N[C@....
24 2J47 Ki = 3.9 uM GDV C17 H21 N4 O5 CC(=O)N[C@....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: LTM; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 LTM 1 1
2 NOK 0.403846 0.895833
3 DJN 0.403846 0.895833
Similar Ligands (3D)
Ligand no: 1; Ligand: LTM; Similar ligands found: 155
No: Ligand Similarity coefficient
1 GDL 1.0000
2 NAG 0.9951
3 NDG 0.9854
4 LOG 0.9826
5 NGA 0.9678
6 BNX 0.9624
7 MAG 0.9613
8 BEU 0.9596
9 NGW 0.9492
10 NGT 0.9468
11 A2G 0.9467
12 SNG 0.9462
13 F34 0.9407
14 BBK 0.9403
15 BM3 0.9361
16 NGO 0.9359
17 HQ6 0.9333
18 GC3 0.9318
19 BGN 0.9299
20 TNX 0.9272
21 6ME 0.9221
22 44V 0.9206
23 327 0.9198
24 5FN 0.9181
25 15N 0.9158
26 0FN 0.9152
27 2F8 0.9147
28 EPR 0.9125
29 2CZ 0.9107
30 NSG 0.9106
31 K82 0.9097
32 GC2 0.9090
33 57O 0.9083
34 HHT 0.9081
35 S8A 0.9065
36 XYH 0.9046
37 6E8 0.9037
38 NBG 0.9037
39 ZZZ 0.9033
40 W81 0.9010
41 GSY 0.9010
42 IAC 0.9009
43 IFG 0.8997
44 X04 0.8995
45 2K8 0.8994
46 JWB 0.8982
47 I4D 0.8973
48 ZPF 0.8951
49 GNL 0.8948
50 PQZ 0.8947
51 APS 0.8944
52 JYT 0.8937
53 CTS 0.8937
54 1BW 0.8930
55 NHT 0.8927
56 SBK 0.8927
57 GCU 0.8923
58 CIP 0.8920
59 F5C 0.8919
60 0JD 0.8914
61 IBM 0.8909
62 GLC 0.8907
63 94B 0.8906
64 ARP 0.8901
65 2LB 0.8901
66 STZ 0.8901
67 PLP 0.8900
68 61M 0.8900
69 LIP 0.8894
70 948 0.8893
71 3XR 0.8882
72 IFL 0.8881
73 JXK 0.8877
74 JVN 0.8870
75 H4B 0.8860
76 9GP 0.8850
77 K3Q 0.8847
78 NB1 0.8841
79 MP5 0.8840
80 NOJ 0.8837
81 2L3 0.8835
82 X05 0.8832
83 BDP 0.8830
84 X09 0.8821
85 BGC 0.8819
86 PRZ 0.8819
87 OMD 0.8819
88 PMP 0.8816
89 TSR 0.8814
90 NLA 0.8811
91 CR1 0.8803
92 PZP 0.8798
93 LGC 0.8794
94 GCB 0.8788
95 GF1 0.8788
96 GAL 0.8787
97 NFM 0.8787
98 YX1 0.8781
99 6FZ 0.8779
100 BMA 0.8772
101 G3F 0.8771
102 NHG 0.8765
103 5OF 0.8765
104 SOE 0.8752
105 GZQ 0.8750
106 JXZ 0.8749
107 HQ9 0.8749
108 MMA 0.8746
109 G6P 0.8746
110 BCU 0.8745
111 ASO 0.8738
112 S24 0.8735
113 ICB 0.8734
114 3C4 0.8732
115 LCN 0.8724
116 NOY 0.8718
117 FSW 0.8718
118 BHS 0.8711
119 8S0 0.8711
120 G1P 0.8702
121 CPW 0.8699
122 SIZ 0.8690
123 JVS 0.8686
124 RVE 0.8682
125 MIG 0.8679
126 AFR 0.8679
127 X0T 0.8677
128 JXW 0.8668
129 9KH 0.8667
130 6HP 0.8660
131 TAG 0.8660
132 CIT 0.8657
133 PYU 0.8654
134 X1P 0.8650
135 NVU 0.8645
136 HA5 0.8645
137 PA1 0.8644
138 GLF 0.8631
139 YO5 0.8624
140 G2F 0.8621
141 GLO 0.8616
142 GLA 0.8610
143 J01 0.8599
144 NZ9 0.8592
145 9FQ 0.8591
146 EMZ 0.8588
147 GFP 0.8584
148 MQB 0.8577
149 HWD 0.8574
150 RGY 0.8573
151 CDI 0.8571
152 L21 0.8571
153 2P3 0.8562
154 H62 0.8534
155 S3C 0.8517
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5ABH; Ligand: YWN; 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: 5abh.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5ABH; Ligand: YWN; Similar sites found with APoc: 4
This union binding pocket(no: 2) in the query (biounit: 5abh.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 5M7S NHT 20.7989
2 5M7S NHT 20.7989
3 5UN9 NHT 29.9603
4 5UN9 NHT 29.9603
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