Receptor
PDB id Resolution Class Description Source Keywords
4PCS 1.77 Å EC: 3.2.1.51 CRYSTAL STRUCTURE OF A BACTERIAL FUCOSIDASE WITH IMINOSUGAR 5S)-3,4-DIHYDROXY-2-[2'-PHENYL]ETHYNYL-5-METHYLPYRROLIDINE BACTEROIDES THETAIOTAOMICRON A-L-FUCOSIDASE ENZYME INHIBITION HYDROLASE
Ref.: EXPLOITING THE HYDROPHOBIC TERRAIN IN FUCOSIDASES W ARYL-SUBSTITUTED PYRROLIDINE IMINOSUGARS. CHEMBIOCHEM V. 16 277 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IMD B:504;
A:504;
C:502;
B:503;
A:503;
D:502;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
69.085 C3 H5 N2 c1c[n...
2M7 C:503;
A:505;
D:503;
B:505;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
217.264 C13 H15 N O2 C[C@H...
SO4 B:501;
C:501;
D:501;
B:502;
A:501;
A:502;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2XIB 2.2 Å EC: 3.2.1.51 CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH D EOXYFUCONOJIRIMYCIN BACTEROIDES THETAIOTAOMICRON FUCOSIDASE HYDROLASE METAL BINDING INHIBITORS
Ref.: STRUCTURAL AND THERMODYNAMIC ANALYSES OF ALPHA-L-FU INHIBITORS. CHEMBIOCHEM V. 11 1971 2010
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4PEE - 2OX C13 H16 N4 O2 C[C@H]1[C@....
2 2XII Kd = 63.3 nM TA9 C21 H22 N2 O5 C[C@H]1[C@....
3 2WVS - FUF C6 H11 F O4 C[C@H]1[C@....
4 2WVU - JFZ C12 H15 N O7 C[C@H]1[C@....
5 4J28 Ki = 2 uM EAT C12 H15 N3 O2 C[C@H]1[C@....
6 6HZY Ki = 121 uM GYZ C13 H16 N2 O6 C[C@H]1[C@....
7 4JFT Ki = 3.5 uM 1KN C12 H17 N O3 C[C@H]1[C@....
8 4PCS - 2M7 C13 H15 N O2 C[C@H]1[C@....
9 4JFU - K80 C12 H17 N O2 Cc1ccc(cc1....
10 4JFV Ki = 0.52 uM H57 C18 H26 Fe N2 O2 CC1C(C(C(N....
11 2XIB Kd = 55.1 nM DFU C6 H13 N O3 C[C@H]1[C@....
12 4PCT - H76 C7 H11 N O2 C[C@H]1[C@....
13 4JFS Ki = 5.4 uM 16Z C13 H19 N O3 C[C@H]1[C@....
14 4JFW Ki = 0.46 uM H58 C20 H30 Fe N2 O2 CC1C(C(C(N....
15 2WVT Kd = 755 nM FHN C7 H16 N O5 C([C@H]1[C....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4PEE - 2OX C13 H16 N4 O2 C[C@H]1[C@....
2 2XII Kd = 63.3 nM TA9 C21 H22 N2 O5 C[C@H]1[C@....
3 2WVS - FUF C6 H11 F O4 C[C@H]1[C@....
4 2WVU - JFZ C12 H15 N O7 C[C@H]1[C@....
5 4J28 Ki = 2 uM EAT C12 H15 N3 O2 C[C@H]1[C@....
6 6HZY Ki = 121 uM GYZ C13 H16 N2 O6 C[C@H]1[C@....
7 4JFT Ki = 3.5 uM 1KN C12 H17 N O3 C[C@H]1[C@....
8 4PCS - 2M7 C13 H15 N O2 C[C@H]1[C@....
9 4JFU - K80 C12 H17 N O2 Cc1ccc(cc1....
10 4JFV Ki = 0.52 uM H57 C18 H26 Fe N2 O2 CC1C(C(C(N....
11 2XIB Kd = 55.1 nM DFU C6 H13 N O3 C[C@H]1[C@....
12 4PCT - H76 C7 H11 N O2 C[C@H]1[C@....
13 4JFS Ki = 5.4 uM 16Z C13 H19 N O3 C[C@H]1[C@....
14 4JFW Ki = 0.46 uM H58 C20 H30 Fe N2 O2 CC1C(C(C(N....
15 2WVT Kd = 755 nM FHN C7 H16 N O5 C([C@H]1[C....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4PEE - 2OX C13 H16 N4 O2 C[C@H]1[C@....
2 2XII Kd = 63.3 nM TA9 C21 H22 N2 O5 C[C@H]1[C@....
3 2WVS - FUF C6 H11 F O4 C[C@H]1[C@....
4 2WVU - JFZ C12 H15 N O7 C[C@H]1[C@....
5 4J28 Ki = 2 uM EAT C12 H15 N3 O2 C[C@H]1[C@....
6 6HZY Ki = 121 uM GYZ C13 H16 N2 O6 C[C@H]1[C@....
7 4JFT Ki = 3.5 uM 1KN C12 H17 N O3 C[C@H]1[C@....
8 4PCS - 2M7 C13 H15 N O2 C[C@H]1[C@....
9 4JFU - K80 C12 H17 N O2 Cc1ccc(cc1....
10 4JFV Ki = 0.52 uM H57 C18 H26 Fe N2 O2 CC1C(C(C(N....
11 2XIB Kd = 55.1 nM DFU C6 H13 N O3 C[C@H]1[C@....
12 4PCT - H76 C7 H11 N O2 C[C@H]1[C@....
13 4JFS Ki = 5.4 uM 16Z C13 H19 N O3 C[C@H]1[C@....
14 4JFW Ki = 0.46 uM H58 C20 H30 Fe N2 O2 CC1C(C(C(N....
15 2WVT Kd = 755 nM FHN C7 H16 N O5 C([C@H]1[C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 2M7; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 2M7 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 2M7; Similar ligands found: 169
No: Ligand Similarity coefficient
1 ARG 1.0000
2 EAT 0.9454
3 AOY 0.9347
4 47V 0.9333
5 OJD 0.9325
6 0OP 0.9301
7 11X 0.9284
8 CBE 0.9280
9 EMU 0.9241
10 3IP 0.9234
11 9JT 0.9226
12 LJ1 0.9210
13 LR2 0.9191
14 TPM 0.9190
15 A51 0.9165
16 STL 0.9150
17 2OX 0.9119
18 LJ2 0.9093
19 1KN 0.9068
20 WCU 0.9068
21 RE2 0.9061
22 CMG 0.9041
23 IEE 0.9032
24 RDV 0.9015
25 FY8 0.9001
26 8KW 0.8999
27 KPV 0.8993
28 MJW 0.8991
29 68B 0.8990
30 0ON 0.8984
31 3CX 0.8981
32 FHV 0.8976
33 BVB 0.8969
34 D8B 0.8964
35 EDG AHR 0.8963
36 6H2 0.8947
37 P2L 0.8939
38 C4E 0.8935
39 PZX 0.8931
40 S7D 0.8927
41 NW1 0.8920
42 0X2 0.8902
43 6C4 0.8897
44 QME 0.8895
45 GJB 0.8893
46 IMK 0.8889
47 SB7 0.8884
48 TH1 0.8878
49 7G0 0.8875
50 EEY 0.8871
51 5TO 0.8867
52 245 0.8867
53 PIT 0.8861
54 L2K 0.8861
55 MR5 0.8858
56 37E 0.8856
57 83D 0.8853
58 AHR AHR 0.8848
59 6C5 0.8844
60 6DQ 0.8841
61 WA2 0.8839
62 F18 0.8831
63 U13 0.8831
64 6C9 0.8829
65 IW1 0.8824
66 WA1 0.8820
67 XYS XYP 0.8819
68 KVD 0.8818
69 531 0.8817
70 7ZO 0.8808
71 0SY 0.8807
72 ERZ 0.8806
73 S0A 0.8806
74 BSU 0.8803
75 H35 0.8799
76 16Z 0.8796
77 ZYC 0.8795
78 5WK 0.8793
79 S8P 0.8791
80 IW4 0.8786
81 IPJ 0.8774
82 YIP 0.8770
83 K80 0.8768
84 2L1 0.8760
85 DZ2 0.8756
86 API 0.8755
87 6CL 0.8754
88 S0B 0.8753
89 XIL 0.8751
90 XDL XYP 0.8751
91 NK5 0.8751
92 MR4 0.8750
93 0XR 0.8743
94 XYP XYP 0.8737
95 S0D 0.8735
96 6BK 0.8732
97 7EH 0.8730
98 6C8 0.8720
99 JBB 0.8718
100 Q2S 0.8717
101 3D8 0.8712
102 IW3 0.8710
103 JMG 0.8707
104 NXY 0.8706
105 IW5 0.8702
106 2LT 0.8699
107 XYS XYS 0.8696
108 6J5 0.8695
109 NX1 0.8694
110 NXB 0.8692
111 6FG 0.8683
112 4BX 0.8682
113 38E 0.8682
114 XYP XDN 0.8680
115 FYR 0.8680
116 AVX 0.8676
117 NIY 0.8676
118 ZEA 0.8675
119 UN4 0.8674
120 0QA 0.8673
121 8M5 0.8671
122 K0G 0.8670
123 GAT 0.8668
124 BG8 0.8660
125 REG 0.8658
126 1HP 0.8657
127 MR6 0.8656
128 5VU 0.8654
129 IW2 0.8653
130 0DF 0.8651
131 NE2 0.8649
132 1PS 0.8647
133 613 0.8642
134 7FZ 0.8642
135 8CC 0.8642
136 1Q4 0.8632
137 LJ5 0.8631
138 ZTW 0.8630
139 KLS 0.8630
140 1Q1 0.8630
141 536 0.8628
142 5E5 0.8627
143 GJG 0.8626
144 2P3 0.8621
145 4FP 0.8619
146 7L4 0.8605
147 LZ5 0.8603
148 DZ1 0.8600
149 TZP 0.8598
150 OAK 0.8598
151 NAR 0.8596
152 UAY 0.8595
153 4AU 0.8592
154 DAH 0.8591
155 4EU 0.8588
156 N2Y 0.8584
157 4P9 0.8573
158 DFL 0.8565
159 QTD 0.8562
160 5P7 0.8557
161 ZIP 0.8555
162 BTN 0.8554
163 GO5 0.8550
164 0OO 0.8543
165 A4V 0.8533
166 IIH 0.8529
167 G14 0.8520
168 FER 0.8515
169 TRP 0.8510
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2XIB; Ligand: DFU; 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: 2xib.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2XIB; Ligand: DFU; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2xib.bio4) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2XIB; Ligand: DFU; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2xib.bio3) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2XIB; Ligand: DFU; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2xib.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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