Receptor
PDB id Resolution Class Description Source Keywords
4QEH 1.55 Å EC: 5.3.1.5 ROOM TEMPERATURE X-RAY STRUCTURE OF D-XYLOSE ISOMERASE IN CO TWO MG2+ IONS AND L-RIBOSE STREPTOMYCES RUBIGINOSUS TIM BARREL SUGAR ISOMERASE MONOSACCHARIDES ISOMERASE
Ref.: L-ARABINOSE BINDING, ISOMERIZATION, AND EPIMERIZATI D-XYLOSE ISOMERASE: X-RAY/NEUTRON CRYSTALLOGRAPHIC MOLECULAR SIMULATION STUDY. STRUCTURE V. 22 1287 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:401;
A:402;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
32O A:403;
Valid;
none;
submit data
150.13 C5 H10 O5 C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2GYI 1.6 Å EC: 5.3.1.5 DESIGN, SYNTHESIS, AND CHARACTERIZATION OF A POTENT XYLOSE I INHIBITOR, D-THREONOHYDROXAMIC ACID, AND HIGH-RESOLUTION X-C RYSTALLOGRAPHIC STRUCTURE OF THE ENZYME-INHIBITOR COMPLEX STREPTOMYCES OLIVOCHROMOGENES ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Ref.: DESIGN, SYNTHESIS, AND CHARACTERIZATION OF A POTENT ISOMERASE INHIBITOR, D-THREONOHYDROXAMIC ACID, AND HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHIC STRUCTURE OF ENZYME-INHIBITOR COMPLEX BIOCHEMISTRY V. 34 3742 1995
Members (39)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1S5M - GLC C6 H12 O6 C([C@@H]1[....
2 3KBM - GLC C6 H12 O6 C([C@@H]1[....
3 4QEH - 32O C5 H10 O5 C([C@H]1[C....
4 3U3H - 03W C3 H8 O4 C([C@H](C(....
5 1XID - ASC C6 H8 O6 C([C@@H]([....
6 4DUO - XYL C5 H12 O5 C([C@@H](C....
7 4QE5 - RUU C5 H10 O5 C1[C@@H]([....
8 6RNF - GLC C6 H12 O6 C([C@@H]1[....
9 1XIH - SOR C6 H14 O6 C([C@@H]([....
10 4ZBC - GLC C6 H12 O6 C([C@@H]1[....
11 4QEE - Z6J C5 H10 O5 C([C@H]1[C....
12 1XIG - XYL C5 H12 O5 C([C@@H](C....
13 1XYC - 3MF C7 H14 O6 CO[C@@H]([....
14 5ZYE - GLC C6 H12 O6 C([C@@H]1[....
15 2XIS - XYL C5 H12 O5 C([C@@H](C....
16 1XYM - GLO C6 H12 O6 C([C@H]([C....
17 8XIA - XLS C5 H10 O5 C([C@H]([C....
18 1XIJ - THE C4 H7 O5 C([C@H]([C....
19 4XIS - XLS C5 H10 O5 C([C@H]([C....
20 1GW9 - LXC C5 H10 O5 C1[C@@H]([....
21 1XIC - XLS C5 H10 O5 C([C@H]([C....
22 1XII - XUL C5 H10 O5 C([C@H]([C....
23 6QNI - GLC C6 H12 O6 C([C@@H]1[....
24 4ZB5 - GLC C6 H12 O6 C([C@@H]1[....
25 1XYB - GLO C6 H12 O6 C([C@H]([C....
26 4ZB2 - FRU C6 H12 O6 C([C@@H]1[....
27 6QNJ - GLC C6 H12 O6 C([C@@H]1[....
28 4QE4 - 34V C5 H10 O5 C1[C@@H]([....
29 4ZB0 - GLC C6 H12 O6 C([C@@H]1[....
30 2GYI Ki = 100 nM HYA C4 H9 N O5 C([C@H]([C....
31 4QE1 - RUU C5 H10 O5 C1[C@@H]([....
32 6RND - GLC C6 H12 O6 C([C@@H]1[....
33 1S5N - XYL C5 H12 O5 C([C@@H](C....
34 1XIF - GLC C6 H12 O6 C([C@@H]1[....
35 3XIS - XLS C5 H10 O5 C([C@H]([C....
36 6QND - GLO C6 H12 O6 C([C@H]([C....
37 1XIE - ASO C6 H12 O5 C1[C@@H]([....
38 3KBN - GLO C6 H12 O6 C([C@H]([C....
39 6QNC - GLC C6 H12 O6 C([C@@H]1[....
70% Homology Family (59)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1S5M - GLC C6 H12 O6 C([C@@H]1[....
2 3KBM - GLC C6 H12 O6 C([C@@H]1[....
3 4QEH - 32O C5 H10 O5 C([C@H]1[C....
4 3U3H - 03W C3 H8 O4 C([C@H](C(....
5 1XID - ASC C6 H8 O6 C([C@@H]([....
6 4DUO - XYL C5 H12 O5 C([C@@H](C....
7 4QE5 - RUU C5 H10 O5 C1[C@@H]([....
8 6RNF - GLC C6 H12 O6 C([C@@H]1[....
9 1XIH - SOR C6 H14 O6 C([C@@H]([....
10 4ZBC - GLC C6 H12 O6 C([C@@H]1[....
11 4QEE - Z6J C5 H10 O5 C([C@H]1[C....
12 1XIG - XYL C5 H12 O5 C([C@@H](C....
13 1XYC - 3MF C7 H14 O6 CO[C@@H]([....
14 5ZYE - GLC C6 H12 O6 C([C@@H]1[....
15 2XIS - XYL C5 H12 O5 C([C@@H](C....
16 1XYM - GLO C6 H12 O6 C([C@H]([C....
17 8XIA - XLS C5 H10 O5 C([C@H]([C....
18 1XIJ - THE C4 H7 O5 C([C@H]([C....
19 4XIS - XLS C5 H10 O5 C([C@H]([C....
20 1GW9 - LXC C5 H10 O5 C1[C@@H]([....
21 1XIC - XLS C5 H10 O5 C([C@H]([C....
22 1XII - XUL C5 H10 O5 C([C@H]([C....
23 6QNI - GLC C6 H12 O6 C([C@@H]1[....
24 4ZB5 - GLC C6 H12 O6 C([C@@H]1[....
25 1XYB - GLO C6 H12 O6 C([C@H]([C....
26 4ZB2 - FRU C6 H12 O6 C([C@@H]1[....
27 6QNJ - GLC C6 H12 O6 C([C@@H]1[....
28 4QE4 - 34V C5 H10 O5 C1[C@@H]([....
29 4ZB0 - GLC C6 H12 O6 C([C@@H]1[....
30 2GYI Ki = 100 nM HYA C4 H9 N O5 C([C@H]([C....
31 4QE1 - RUU C5 H10 O5 C1[C@@H]([....
32 6RND - GLC C6 H12 O6 C([C@@H]1[....
33 1S5N - XYL C5 H12 O5 C([C@@H](C....
34 1XIF - GLC C6 H12 O6 C([C@@H]1[....
35 3XIS - XLS C5 H10 O5 C([C@H]([C....
36 6QND - GLO C6 H12 O6 C([C@H]([C....
37 1XIE - ASO C6 H12 O5 C1[C@@H]([....
38 3KBN - GLO C6 H12 O6 C([C@H]([C....
39 6QNC - GLC C6 H12 O6 C([C@@H]1[....
40 1DID - DIG C6 H13 N O4 C([C@H]1[C....
41 1XLC - XYL C5 H12 O5 C([C@@H](C....
42 1XLJ - XYL C5 H12 O5 C([C@@H](C....
43 1DIE - NOJ C6 H13 N O4 C1[C@@H]([....
44 1XLF - GCO C6 H12 O7 C([C@H]([C....
45 4XIA - SOR C6 H14 O6 C([C@@H]([....
46 1XLM - XYL C5 H12 O5 C([C@@H](C....
47 5XIA - XYL C5 H12 O5 C([C@@H](C....
48 1XLI Ki = 33 mM GLT C6 H12 O5 S C([C@@H]1[....
49 1XLG - XYL C5 H12 O5 C([C@@H](C....
50 1XLD - XYL C5 H12 O5 C([C@@H](C....
51 2XIN - SOR C6 H14 O6 C([C@@H]([....
52 8XIM - XLS C5 H10 O5 C([C@H]([C....
53 1XIM - XYL C5 H12 O5 C([C@@H](C....
54 2XIM - XYL C5 H12 O5 C([C@@H](C....
55 1XIN - XYL C5 H12 O5 C([C@@H](C....
56 3XIM - SOR C6 H14 O6 C([C@@H]([....
57 5XIN - XLS C5 H10 O5 C([C@H]([C....
58 9XIM - XLS C5 H10 O5 C([C@H]([C....
59 6XIM - XLS C5 H10 O5 C([C@H]([C....
50% Homology Family (59)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1S5M - GLC C6 H12 O6 C([C@@H]1[....
2 3KBM - GLC C6 H12 O6 C([C@@H]1[....
3 4QEH - 32O C5 H10 O5 C([C@H]1[C....
4 3U3H - 03W C3 H8 O4 C([C@H](C(....
5 1XID - ASC C6 H8 O6 C([C@@H]([....
6 4DUO - XYL C5 H12 O5 C([C@@H](C....
7 4QE5 - RUU C5 H10 O5 C1[C@@H]([....
8 6RNF - GLC C6 H12 O6 C([C@@H]1[....
9 1XIH - SOR C6 H14 O6 C([C@@H]([....
10 4ZBC - GLC C6 H12 O6 C([C@@H]1[....
11 4QEE - Z6J C5 H10 O5 C([C@H]1[C....
12 1XIG - XYL C5 H12 O5 C([C@@H](C....
13 1XYC - 3MF C7 H14 O6 CO[C@@H]([....
14 5ZYE - GLC C6 H12 O6 C([C@@H]1[....
15 2XIS - XYL C5 H12 O5 C([C@@H](C....
16 1XYM - GLO C6 H12 O6 C([C@H]([C....
17 8XIA - XLS C5 H10 O5 C([C@H]([C....
18 1XIJ - THE C4 H7 O5 C([C@H]([C....
19 4XIS - XLS C5 H10 O5 C([C@H]([C....
20 1GW9 - LXC C5 H10 O5 C1[C@@H]([....
21 1XIC - XLS C5 H10 O5 C([C@H]([C....
22 1XII - XUL C5 H10 O5 C([C@H]([C....
23 6QNI - GLC C6 H12 O6 C([C@@H]1[....
24 4ZB5 - GLC C6 H12 O6 C([C@@H]1[....
25 1XYB - GLO C6 H12 O6 C([C@H]([C....
26 4ZB2 - FRU C6 H12 O6 C([C@@H]1[....
27 6QNJ - GLC C6 H12 O6 C([C@@H]1[....
28 4QE4 - 34V C5 H10 O5 C1[C@@H]([....
29 4ZB0 - GLC C6 H12 O6 C([C@@H]1[....
30 2GYI Ki = 100 nM HYA C4 H9 N O5 C([C@H]([C....
31 4QE1 - RUU C5 H10 O5 C1[C@@H]([....
32 6RND - GLC C6 H12 O6 C([C@@H]1[....
33 1S5N - XYL C5 H12 O5 C([C@@H](C....
34 1XIF - GLC C6 H12 O6 C([C@@H]1[....
35 3XIS - XLS C5 H10 O5 C([C@H]([C....
36 6QND - GLO C6 H12 O6 C([C@H]([C....
37 1XIE - ASO C6 H12 O5 C1[C@@H]([....
38 3KBN - GLO C6 H12 O6 C([C@H]([C....
39 6QNC - GLC C6 H12 O6 C([C@@H]1[....
40 1DID - DIG C6 H13 N O4 C([C@H]1[C....
41 1XLC - XYL C5 H12 O5 C([C@@H](C....
42 1XLJ - XYL C5 H12 O5 C([C@@H](C....
43 1DIE - NOJ C6 H13 N O4 C1[C@@H]([....
44 1XLF - GCO C6 H12 O7 C([C@H]([C....
45 4XIA - SOR C6 H14 O6 C([C@@H]([....
46 1XLM - XYL C5 H12 O5 C([C@@H](C....
47 5XIA - XYL C5 H12 O5 C([C@@H](C....
48 1XLI Ki = 33 mM GLT C6 H12 O5 S C([C@@H]1[....
49 1XLG - XYL C5 H12 O5 C([C@@H](C....
50 1XLD - XYL C5 H12 O5 C([C@@H](C....
51 2XIN - SOR C6 H14 O6 C([C@@H]([....
52 8XIM - XLS C5 H10 O5 C([C@H]([C....
53 1XIM - XYL C5 H12 O5 C([C@@H](C....
54 2XIM - XYL C5 H12 O5 C([C@@H](C....
55 1XIN - XYL C5 H12 O5 C([C@@H](C....
56 3XIM - SOR C6 H14 O6 C([C@@H]([....
57 5XIN - XLS C5 H10 O5 C([C@H]([C....
58 9XIM - XLS C5 H10 O5 C([C@H]([C....
59 6XIM - XLS C5 H10 O5 C([C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 32O; Similar ligands found: 106
No: Ligand ECFP6 Tc MDL keys Tc
1 RIB 1 1
2 32O 1 1
3 BDR 1 1
4 FUB 1 1
5 Z6J 1 1
6 AHR 1 1
7 GIV 0.653846 0.866667
8 GLC 0.653846 0.866667
9 BGC 0.653846 0.866667
10 GLA 0.653846 0.866667
11 GXL 0.653846 0.866667
12 MAN 0.653846 0.866667
13 GAL 0.653846 0.866667
14 WOO 0.653846 0.866667
15 ALL 0.653846 0.866667
16 BMA 0.653846 0.866667
17 AHR AHR 0.486486 0.875
18 FUB AHR 0.486486 0.875
19 2H5 0.483871 0.764706
20 PA1 0.483871 0.684211
21 GCS 0.483871 0.684211
22 G2F 0.483871 0.764706
23 GAF 0.483871 0.764706
24 1GN 0.483871 0.684211
25 95Z 0.483871 0.684211
26 SHG 0.483871 0.764706
27 G3F 0.483871 0.764706
28 2FG 0.483871 0.764706
29 X6X 0.483871 0.684211
30 3MG 0.46875 0.764706
31 SR1 0.466667 0.764706
32 2GS 0.454545 0.764706
33 FUB AHR AHR 0.45 0.875
34 AHR AHR AHR AHR AHR AHR 0.45 0.875
35 ABF 0.441176 0.675
36 RP5 0.441176 0.675
37 HSX 0.441176 0.675
38 LBT 0.439024 0.742857
39 B2G 0.439024 0.742857
40 BGC GAL 0.439024 0.742857
41 BMA GAL 0.439024 0.742857
42 GAL BGC 0.439024 0.742857
43 LAT 0.439024 0.742857
44 MAB 0.439024 0.742857
45 CBK 0.439024 0.742857
46 CBI 0.439024 0.742857
47 GLC GAL 0.439024 0.742857
48 BGC BMA 0.439024 0.742857
49 MAL 0.439024 0.742857
50 N9S 0.439024 0.742857
51 BMA BMA 0.439024 0.742857
52 TRE 0.424242 0.742857
53 YIO 0.419355 0.757576
54 GLF 0.40625 0.735294
55 BNX 0.405405 0.619048
56 ALX 0.405405 0.619048
57 M3M 0.404762 0.742857
58 GLC GLC 0.404762 0.742857
59 LB2 0.404762 0.742857
60 NGR 0.404762 0.742857
61 MAN GLC 0.404762 0.742857
62 GLA GAL 0.404762 0.742857
63 GLC BGC 0.404762 0.742857
64 GLA GLA 0.404762 0.742857
65 MTT 0.4 0.742857
66 MAN BMA BMA BMA BMA 0.4 0.742857
67 BGC BGC BGC BGC 0.4 0.742857
68 BMA BMA BMA BMA BMA 0.4 0.742857
69 CEX 0.4 0.742857
70 MAN BMA BMA BMA BMA BMA 0.4 0.742857
71 B4G 0.4 0.742857
72 GLA GAL GLC 0.4 0.742857
73 BGC BGC BGC 0.4 0.742857
74 BGC GLC GLC GLC GLC 0.4 0.742857
75 BGC GLC GLC 0.4 0.742857
76 GLC GLC GLC GLC GLC 0.4 0.742857
77 DXI 0.4 0.742857
78 GLC BGC GLC 0.4 0.742857
79 BMA BMA BMA 0.4 0.742857
80 BMA BMA BMA BMA BMA BMA 0.4 0.742857
81 CTR 0.4 0.742857
82 GLC GAL GAL 0.4 0.742857
83 GAL GAL GAL 0.4 0.742857
84 MAN MAN BMA BMA BMA BMA 0.4 0.742857
85 CTT 0.4 0.742857
86 CT3 0.4 0.742857
87 BGC BGC BGC GLC 0.4 0.742857
88 GLA GAL BGC 0.4 0.742857
89 GLC BGC BGC BGC BGC 0.4 0.742857
90 ASO 0.4 0.757576
91 BMA MAN BMA 0.4 0.742857
92 CE8 0.4 0.742857
93 MLR 0.4 0.742857
94 CE6 0.4 0.742857
95 BGC BGC GLC 0.4 0.742857
96 BGC GLC GLC GLC 0.4 0.742857
97 MAN BMA BMA 0.4 0.742857
98 GLC BGC BGC BGC 0.4 0.742857
99 BGC GLC GLC GLC GLC GLC GLC 0.4 0.742857
100 MT7 0.4 0.742857
101 CE5 0.4 0.742857
102 CEY 0.4 0.742857
103 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.4 0.742857
104 GLC BGC BGC 0.4 0.742857
105 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.4 0.742857
106 GLC BGC BGC BGC BGC BGC 0.4 0.742857
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2GYI; Ligand: HYA; Similar sites found with APoc: 6
This union binding pocket(no: 1) in the query (biounit: 2gyi.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
1 1DE6 RNS 7.51295
2 1DE6 RNS 7.51295
3 1DE6 RNS 7.51295
4 1DE6 RNS 7.51295
5 2I56 RNS 10.8808
6 2I56 RNS 10.8808
Pocket No.: 2; Query (leader) PDB : 2GYI; Ligand: HYA; 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: 2gyi.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2GYI; Ligand: HYA; Similar sites found with APoc: 6
This union binding pocket(no: 3) in the query (biounit: 2gyi.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
1 1DE6 RNS 7.51295
2 1DE6 RNS 7.51295
3 1DE6 RNS 7.51295
4 1DE6 RNS 7.51295
5 2I56 RNS 10.8808
6 2I56 RNS 10.8808
Pocket No.: 4; Query (leader) PDB : 2GYI; Ligand: HYA; 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: 2gyi.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
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