Receptor
PDB id Resolution Class Description Source Keywords
6HZY 1.7 Å EC: 3.2.1.51 CRYSTAL STRUCTURE OF A BACTERIAL FUCOSIDASE WITH INHIBITOR F BACTEROIDES THETAIOTAOMICRON VPI-5482 HYDROLASE
Ref.: SYNTHETIC AND CRYSTALLOGRAPHIC INSIGHT INTO EXPLOIT SP2HYBRIDIZATION IN THE DEVELOPMENT OF ALPHA-L-FUCO INHIBITORS. CHEMBIOCHEM V. 20 1365 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:605;
A:508;
A:507;
A:510;
B:601;
A:506;
A:505;
A:503;
A:509;
B:604;
A:504;
B:602;
A:511;
A:502;
B:603;
B:606;
A:501;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
GYZ A:512;
B:607;
 Valid;
Valid;
 none;
none;
 Ki = 121 uM
296.276 C13 H16 N2 O6 C[C@H...
SO4 A:513;
A:516;
B:609;
B:608;
B:610;
A:514;
A:515;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
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: GYZ; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 GYZ 1 1
2 OAN 0.5 0.864407
3 OGN 0.5 0.864407
4 VPU 0.482353 0.772727
5 NP6 0.481928 0.796875
6 8M7 0.464286 0.822581
7 5G0 GAL 0.4 0.746269
Similar Ligands (3D)
Ligand no: 1; Ligand: GYZ; Similar ligands found: 111
No: Ligand Similarity coefficient
1 JVB 0.9165
2 ZX7 0.9148
3 OA5 0.9119
4 9M9 0.9102
5 KOT 0.9100
6 6MY 0.9091
7 B1W 0.9088
8 KS2 0.9088
9 B1N 0.9072
10 73E 0.9015
11 F5N 0.8997
12 PNG 0.8974
13 F7L 0.8958
14 T5J 0.8949
15 S06 0.8944
16 246 0.8931
17 20P 0.8914
18 CA2 0.8905
19 FVQ 0.8900
20 CWP 0.8898
21 BZD 0.8896
22 28C 0.8892
23 2OX 0.8890
24 9PC 0.8885
25 D9Q 0.8881
26 3X8 0.8871
27 NNF 0.8866
28 MF5 0.8858
29 KUQ 0.8858
30 YC8 0.8854
31 4VC 0.8846
32 MMA DH6 0.8846
33 4KN 0.8844
34 KSY 0.8838
35 9RK 0.8831
36 9EG 0.8820
37 C17 0.8803
38 4P9 0.8799
39 0MB 0.8791
40 YX0 0.8787
41 5RU 0.8784
42 G27 0.8780
43 L02 0.8778
44 BXB 0.8775
45 ZUF 0.8775
46 HCC 0.8769
47 M09 0.8769
48 CMZ 0.8767
49 1UA 0.8766
50 9X0 0.8760
51 M07 0.8760
52 RM8 0.8755
53 F08 0.8753
54 J2W 0.8752
55 M62 0.8751
56 F33 0.8748
57 JP5 0.8742
58 JPW 0.8742
59 F41 0.8739
60 5V3 0.8730
61 E98 0.8730
62 E92 0.8730
63 L43 0.8712
64 JV5 0.8711
65 147 0.8702
66 BCE 0.8697
67 0RU 0.8695
68 9B2 0.8694
69 6NF 0.8694
70 1UT 0.8694
71 HN3 0.8694
72 EBB 0.8690
73 M0V 0.8687
74 MRE 0.8676
75 GAL NPO 0.8674
76 PNJ 0.8672
77 H8B 0.8672
78 5ET 0.8665
79 2ZI 0.8664
80 FO2 0.8659
81 W2E 0.8658
82 0LY 0.8652
83 QDR 0.8651
84 M7C 0.8651
85 IY5 0.8649
86 EX7 0.8648
87 AVQ 0.8646
88 HH7 0.8644
89 10H 0.8637
90 87F 0.8635
91 SNP 0.8629
92 JP8 0.8624
93 87C 0.8620
94 BO1 0.8618
95 5HG 0.8614
96 NQK 0.8614
97 F91 0.8609
98 HA1 0.8606
99 5YA 0.8604
100 C0E 0.8602
101 YH4 0.8589
102 4UZ 0.8585
103 KWK 0.8577
104 SKY 0.8572
105 PNW 0.8571
106 ECZ 0.8565
107 1Q1 0.8564
108 0QX 0.8557
109 FZ8 0.8547
110 JP3 0.8547
111 3PQ 0.8522
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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