Receptor
PDB id Resolution Class Description Source Keywords
2oyk 1.5 Å EC: 3.2.1.123 ENDO-GLYCOCERAMIDASE II FROM RHODOCOCCUS SP.: CELLOBIOSE-LIK ISOFAGOMINE COMPLEX RHODOCOCCUS SP. (ALPHA/BETA)8 (TIM) BARREL HYDROLASE
Ref.: THE STRUCTURAL BASIS OF GLYCOSIDASE INHIBITION BY FIVE-MEMBERED IMINOCYCLITOLS: THE CLAN A GLYCOSIDE ENDOGLYCOCERAMIDASE AS A MODEL SYSTEM. ANGEW.CHEM.INT.ED.ENGL. V. 46 4474 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
9MR A:600;
B:600;
 Valid;
Valid;
 none;
none;
 Ki = 5 uM
309.313 C12 H23 N O8 C1[C@...
GOL A:603;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
NA A:601;
A:602;
B:601;
B:602;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2OYL 1.8 Å EC: 3.2.1.123 ENDO-GLYCOCERAMIDASE II FROM RHODOCOCCUS SP.: CELLOBIOSE-LIK IMIDAZOLE COMPLEX RHODOCOCCUS SP. (ALPHA/BETA)8 (TIM) BARREL HYDROLASE
Ref.: THE STRUCTURAL BASIS OF GLYCOSIDASE INHIBITION BY FIVE-MEMBERED IMINOCYCLITOLS: THE CLAN A GLYCOSIDE ENDOGLYCOCERAMIDASE AS A MODEL SYSTEM. ANGEW.CHEM.INT.ED.ENGL. V. 46 4474 2007
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2OYL Ki = 0.5 uM IDC C14 H22 N2 O9 c1cn2c(n1)....
2 2OSX - BGC 16C GAL SIA n/a n/a
3 2OYM Ki = 10 uM MNI C15 H23 N3 O4 CN(C)c1ccc....
4 2OYK Ki = 5 uM 9MR C12 H23 N O8 C1[C@@H]([....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2OYL Ki = 0.5 uM IDC C14 H22 N2 O9 c1cn2c(n1)....
2 2OSX - BGC 16C GAL SIA n/a n/a
3 2OYM Ki = 10 uM MNI C15 H23 N3 O4 CN(C)c1ccc....
4 2OYK Ki = 5 uM 9MR C12 H23 N O8 C1[C@@H]([....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2OYL Ki = 0.5 uM IDC C14 H22 N2 O9 c1cn2c(n1)....
2 2OSX - BGC 16C GAL SIA n/a n/a
3 2OYM Ki = 10 uM MNI C15 H23 N3 O4 CN(C)c1ccc....
4 2OYK Ki = 5 uM 9MR C12 H23 N O8 C1[C@@H]([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 9MR; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 9MR 1 1
2 G3I 0.836364 0.976744
3 G2I 0.836364 0.976744
4 IFM BGC 0.559322 0.954545
5 ISX 0.559322 0.97619
6 BGC OXZ 0.533333 0.854167
7 BQZ 0.509434 0.714286
8 MAN MNM 0.5 0.78
9 5QP 0.491803 0.744186
10 RR7 GLC 0.483333 0.790698
11 GAL GLA 0.482759 0.744186
12 NOY BGC 0.47619 0.78
13 RZM 0.466667 0.847826
14 MBG GLA 0.465517 0.711111
15 BGC GLA GAL 0.465517 0.744186
16 BGC OXZ BGC 0.463768 0.836735
17 GDQ GLC 0.461538 0.78
18 GLC DMJ 0.453125 0.851064
19 NOJ GLC 0.453125 0.851064
20 GLC IFM 0.453125 0.931818
21 FUC GAL 0.451613 0.704545
22 GLC 7LQ 0.446154 0.704545
23 ABL 0.446154 0.78
24 BGC BGC BGC BGC BGC 0.444444 0.744186
25 BGC BGC BGC 0.444444 0.744186
26 BGC BGC BGC BGC BGC BGC 0.444444 0.744186
27 BGC BGC BGC BGC BGC BGC BGC 0.444444 0.744186
28 GLC BGC BGC BGC 0.444444 0.744186
29 MBG GAL 0.442623 0.711111
30 MGL GAL 0.442623 0.711111
31 7D1 MAN 0.435484 0.75
32 MAN BMA BMA 0.432836 0.75
33 GLC GLC GLC GLC BGC GLC GLC 0.428571 0.744186
34 MAN BMA BMA BMA BMA BMA BMA 0.428571 0.744186
35 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.428571 0.744186
36 MAN MAN 0.42623 0.744186
37 CJX 0.424242 0.795918
38 GCU BGC 0.424242 0.688889
39 MAN IPD MAN 0.421875 0.615385
40 FRU BMA 0.421875 0.717391
41 MAN G63 0.41791 0.8
42 GLC EDO GLC 0.415385 0.75
43 MAN MAN BMA 0.414286 0.75
44 A2G GAL 0.411765 0.74
45 AHR FUB 0.410714 0.644444
46 BMA MAN MAN 0.405797 0.744186
47 BGC XGP 0.402985 0.615385
48 DGO MAN 0.4 0.727273
Similar Ligands (3D)
Ligand no: 1; Ligand: 9MR; Similar ligands found: 94
No: Ligand Similarity coefficient
1 BGC BGC 0.9638
2 BMA BGC 0.9583
3 GCS GCS 0.9571
4 SHG BGC 0.9555
5 IFM BMA 0.9551
6 BMA IFM 0.9551
7 GLC GLC 0.9514
8 GLC BGC 0.9504
9 PA1 GCS 0.9482
10 SA0 0.9458
11 GLC GAL 0.9371
12 BGC GAL 0.9354
13 BMA BMA 0.9319
14 SGC BGC 0.9245
15 BMA GAL 0.9236
16 BGC Z9D 0.9209
17 MAN BMA 0.9201
18 MGL SGC 0.9178
19 636 0.9130
20 BEM BEM 0.9108
21 64I 0.9021
22 FRU GAL 0.9009
23 6EN 0.8995
24 MHD GAL 0.8984
25 6GR 0.8982
26 683 0.8966
27 GLO BGC 0.8964
28 CJZ 0.8958
29 145 0.8951
30 MAV BEM 0.8949
31 IDC 0.8939
32 6J3 0.8904
33 FHI 0.8902
34 BNY 0.8876
35 D2M 0.8872
36 43S 0.8868
37 BRY 0.8867
38 XYP XYP 0.8858
39 ZT2 0.8853
40 Q11 0.8842
41 XIF XYP 0.8833
42 OFL 0.8832
43 TLF 0.8827
44 XIL 0.8826
45 XDL XYP 0.8826
46 3WJ 0.8826
47 17C 0.8821
48 ID8 0.8818
49 U19 0.8806
50 XYP XIF 0.8804
51 1FL 0.8790
52 38E 0.8788
53 A4G 0.8774
54 MYG 0.8759
55 IXM 0.8759
56 XYP AHR 0.8757
57 GAL NGT 0.8750
58 FLF 0.8747
59 BGC GLC 0.8746
60 4GU 0.8746
61 BXZ 0.8726
62 BEM LGU 0.8722
63 XYP XDN 0.8715
64 K3Q 7CV 0.8710
65 EAJ 0.8710
66 MQS 0.8698
67 MVL BMA 0.8695
68 LI4 0.8691
69 XYS XYS 0.8688
70 F01 0.8682
71 9FN 0.8676
72 272 0.8674
73 WVV 0.8671
74 THM 0.8669
75 GAT 0.8656
76 SGC GLC 0.8651
77 Z15 0.8645
78 P2L 0.8641
79 SGV 0.8640
80 AOD 0.8630
81 NFL 0.8625
82 P2C 0.8624
83 Z16 0.8620
84 9CE 0.8618
85 XYS XYP 0.8608
86 NGT GAL 0.8598
87 Z57 0.8592
88 GAL NOK 0.8582
89 NEO 0.8572
90 LGU MAW 0.8571
91 2QU 0.8559
92 BMA MVL 0.8546
93 4L2 0.8543
94 TOP 0.8516
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2OYL; Ligand: IDC; 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: 2oyl.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2OYL; Ligand: IDC; 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: 2oyl.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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