Receptor
PDB id Resolution Class Description Source Keywords
4AIU 2.25 Å EC: 3.2.1.52 A COMPLEX STRUCTURE OF BTGH84 BACTEROIDES THETAIOTAOMICRON VPI-5482 HYDROLASE GLYCOSIDE HYDROLASE INHIBITOR COMPLEX
Ref.: METABOLISM OF VERTEBRATE AMINO SUGARS WITH N-GLYCOL GROUPS: INTRACELLULAR BETA-O-LINKED N-GLYCOLYLGLUCO (GLCNGC), UDP-GLCNGC, AND THE BIOCHEMICAL AND STRUC RATIONALE FOR THE SUBSTRATE TOLERANCE OF BETA-O-LIN BETA-N-ACETYLGLUCOSAMINIDASE. J.BIOL.CHEM.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1590;
 Part of Protein;
 none;
 submit data
40.078 Ca [Ca+2...
GC3 A:1589;
 Valid;
 none;
 submit data
219.192 C8 H13 N O6 C([C@...
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: GC3; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 GC3 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: GC3; Similar ligands found: 206
No: Ligand Similarity coefficient
1 NGT 0.9786
2 NGO 0.9762
3 NGW 0.9655
4 NHT 0.9576
5 NB1 0.9521
6 TNX 0.9506
7 5FN 0.9492
8 NAG 0.9434
9 G1P 0.9429
10 NSG 0.9375
11 LTM 0.9318
12 GDL 0.9314
13 GPM 0.9271
14 NOK 0.9270
15 UFO 0.9270
16 NDG 0.9245
17 GNL 0.9227
18 JV4 0.9216
19 SRO 0.9189
20 K3Q 0.9175
21 PH2 0.9172
22 JTH 0.9157
23 R1P 0.9131
24 MS9 0.9130
25 GFP 0.9123
26 ZZZ 0.9118
27 327 0.9116
28 57O 0.9115
29 IFG 0.9102
30 YTX 0.9092
31 R9Y 0.9092
32 6ME 0.9078
33 ASC 0.9064
34 5WU 0.9061
35 CKU 0.9059
36 H7Y 0.9056
37 44V 0.9049
38 BM3 0.9036
39 2C2 0.9034
40 TXW 0.9025
41 IOP 0.9021
42 9R5 0.9014
43 CTS 0.9004
44 BEU 0.8998
45 EN1 0.8996
46 LOG 0.8995
47 HHR 0.8983
48 NPA 0.8982
49 9KH 0.8981
50 EMZ 0.8978
51 JVN 0.8976
52 BDP 0.8972
53 F34 0.8960
54 TLM 0.8949
55 GC2 0.8949
56 CIP 0.8949
57 TRP 0.8943
58 OMD 0.8942
59 AEH 0.8938
60 HA5 0.8933
61 BGC 0.8932
62 9VZ 0.8932
63 EPR 0.8931
64 M1P 0.8927
65 ALE 0.8927
66 15N 0.8922
67 4V6 0.8919
68 FER 0.8914
69 5OF 0.8914
70 7MK 0.8913
71 3CU 0.8904
72 GLC 0.8895
73 2K8 0.8894
74 3C4 0.8889
75 6VD 0.8885
76 293 0.8880
77 S8D 0.8878
78 GLG 0.8869
79 JVA 0.8869
80 J6W 0.8867
81 ODO 0.8865
82 NGA 0.8863
83 VOH 0.8861
84 0JD 0.8859
85 9BF 0.8858
86 TL6 0.8858
87 SLC 0.8857
88 3RI 0.8854
89 5GU 0.8854
90 BCU 0.8853
91 DHY 0.8849
92 G6P 0.8849
93 DEW 0.8849
94 X09 0.8845
95 XQI 0.8845
96 HPT 0.8837
97 MMA 0.8834
98 PLP 0.8834
99 BQ2 0.8830
100 APS 0.8829
101 IAC 0.8828
102 8VR 0.8826
103 3Y7 0.8823
104 OSB 0.8822
105 SOE 0.8818
106 W81 0.8815
107 61M 0.8815
108 2FY 0.8803
109 MPP 0.8800
110 BGP 0.8795
111 KG1 0.8784
112 ASO 0.8782
113 DEG 0.8781
114 F6P 0.8779
115 CEG 0.8773
116 2UZ 0.8771
117 C9E 0.8770
118 NOJ 0.8769
119 XYH 0.8761
120 PW1 0.8761
121 L21 0.8759
122 X8Z 0.8756
123 M6P 0.8755
124 LYL 0.8754
125 RVE 0.8752
126 SIZ 0.8751
127 9F8 0.8750
128 ISD 0.8748
129 F1X 0.8748
130 STT 0.8748
131 PMP 0.8745
132 CHQ 0.8744
133 GLP 0.8740
134 TLE 0.8737
135 PYU 0.8735
136 F5C 0.8735
137 A2G 0.8734
138 TAG 0.8734
139 DCZ 0.8731
140 PLR 0.8729
141 NLA 0.8723
142 46M 0.8722
143 LNR 0.8722
144 H4B 0.8722
145 7MX 0.8721
146 BBK 0.8718
147 REL 0.8717
148 2CZ 0.8714
149 HQ6 0.8711
150 SNG 0.8708
151 3LJ 0.8707
152 CCV 0.8707
153 GZQ 0.8704
154 7QS 0.8701
155 PXP 0.8701
156 TYR 0.8698
157 0FN 0.8697
158 NFM 0.8692
159 ICB 0.8691
160 NVU 0.8690
161 P7Y 0.8683
162 BG6 0.8683
163 K82 0.8681
164 D6G 0.8680
165 2EC 0.8676
166 67Y 0.8673
167 5WZ 0.8672
168 6HP 0.8670
169 M02 0.8669
170 CLU 0.8666
171 JXZ 0.8665
172 6J9 0.8663
173 HHT 0.8662
174 AFR 0.8660
175 M74 0.8658
176 6Q3 0.8653
177 4R1 0.8653
178 DUR 0.8653
179 GLR 0.8648
180 54Z 0.8638
181 FTV 0.8636
182 S8A 0.8634
183 XDE 0.8633
184 TSR 0.8623
185 MP5 0.8622
186 HL4 0.8620
187 KIF 0.8618
188 TZM 0.8614
189 G2F 0.8611
190 SLY 0.8610
191 NIY 0.8603
192 948 0.8601
193 M5H 0.8593
194 3IL 0.8586
195 LTN 0.8579
196 NOY 0.8576
197 2UB 0.8566
198 AZY 0.8563
199 HJH 0.8542
200 QIF 0.8542
201 FHN 0.8541
202 GTC 0.8539
203 YX1 0.8527
204 TOM 0.8520
205 AVO 0.8510
206 P0P 0.8505
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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