Receptor
PDB id Resolution Class Description Source Keywords
2WBK 2.1 Å EC: 3.2.1.25 STRUCTURE OF THE MICHAELIS COMPLEX OF BETA-MANNOSIDASE, MAN2A, PROVIDES INSIGHT INTO THE CONFORMATIONAL ITINERARY O F MANNOSIDE HYDROLYSIS BACTEROIDES THETAIOTAOMICRON GLYCOSIDE HYDROLASE CONFORMATIONAL ITINERARY HYDROLASE MANNOSIDASE BETA-MANNOSIDE MICHAELIS COMPLEX
Ref.: STRUCTURE OF THE MICHAELIS COMPLEX OF BETA-MANNOSIDASE, MAN2A, PROVIDES INSIGHT INTO THE CONFORMATIONAL ITINERARY OF MANNOSIDE HYDROLYSIS. CELL(CAMBRIDGE,MASS.) V. 18 2484 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BR A:1881;
A:1882;
A:1883;
A:1884;
A:1885;
A:1890;
B:1881;
B:1882;
B:1883;
B:1884;
B:1888;
B:1890;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
79.904 Br [Br-]
CL A:1867;
A:1880;
A:1893;
A:1894;
B:1885;
B:1886;
B:1893;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
EDO A:1865;
A:1866;
A:1868;
A:1870;
A:1871;
A:1872;
A:1873;
A:1874;
A:1875;
A:1876;
A:1877;
A:1878;
A:1879;
A:1886;
A:1887;
A:1888;
A:1889;
A:1891;
A:1892;
B:1867;
B:1869;
B:1870;
B:1871;
B:1872;
B:1873;
B:1874;
B:1875;
B:1876;
B:1877;
B:1878;
B:1879;
B:1880;
B:1887;
B:1889;
B:1891;
B:1892;
B:1894;
B:1895;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
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;
none;
none;
none;
none;
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)...
M2F A:1869;
B:1868;
Valid;
Valid;
none;
none;
submit data
348.238 C12 H13 F N2 O9 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VOT 1.95 Å EC: 3.2.1.25 STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES BACTEROIDES THETAIOTAOMICRON LINEAR FREE ENERGY RELATIONSHIP HYDROLASE TRANSITION STATE MIMIC MANNOSIDASE GLYCOSIDE HYDROLASE
Ref.: STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES. NAT.CHEM.BIOL. V. 4 306 2008
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2VQU Ki = 975 nM NOY C6 H13 N O4 C1C(C(C(C(....
2 2VR4 Ki = 2.1 uM 17B C10 H21 N3 O4 C(CCN=C1C(....
3 2VO5 Ki = 13 uM VBZ C15 H21 N O4 c1ccc(cc1)....
4 2VQT Ki = 1 uM 15A C8 H17 N3 O4 C(CN=C1C(C....
5 2VL4 Ki = 975 nM MNM C6 H13 N O4 C1C(C(C(C(....
6 2VOT Ki = 72 nM NHV C15 H20 N3 O4 c1ccc(cc1)....
7 2VMF Ki = 1400 nM MVL C8 H12 N2 O4 c1cn2c(n1)....
8 2WBK - M2F C12 H13 F N2 O9 c1cc(c(cc1....
9 2VJX Ki = 11 uM IFL C6 H11 N O4 C1C(C(C(C(....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2VQU Ki = 975 nM NOY C6 H13 N O4 C1C(C(C(C(....
2 2VR4 Ki = 2.1 uM 17B C10 H21 N3 O4 C(CCN=C1C(....
3 2VO5 Ki = 13 uM VBZ C15 H21 N O4 c1ccc(cc1)....
4 2VQT Ki = 1 uM 15A C8 H17 N3 O4 C(CN=C1C(C....
5 2VL4 Ki = 975 nM MNM C6 H13 N O4 C1C(C(C(C(....
6 2VOT Ki = 72 nM NHV C15 H20 N3 O4 c1ccc(cc1)....
7 2VMF Ki = 1400 nM MVL C8 H12 N2 O4 c1cn2c(n1)....
8 2WBK - M2F C12 H13 F N2 O9 c1cc(c(cc1....
9 2VJX Ki = 11 uM IFL C6 H11 N O4 C1C(C(C(C(....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2VQU Ki = 975 nM NOY C6 H13 N O4 C1C(C(C(C(....
2 2VR4 Ki = 2.1 uM 17B C10 H21 N3 O4 C(CCN=C1C(....
3 2VO5 Ki = 13 uM VBZ C15 H21 N O4 c1ccc(cc1)....
4 2VQT Ki = 1 uM 15A C8 H17 N3 O4 C(CN=C1C(C....
5 2VL4 Ki = 975 nM MNM C6 H13 N O4 C1C(C(C(C(....
6 2VOT Ki = 72 nM NHV C15 H20 N3 O4 c1ccc(cc1)....
7 2VMF Ki = 1400 nM MVL C8 H12 N2 O4 c1cn2c(n1)....
8 2WBK - M2F C12 H13 F N2 O9 c1cc(c(cc1....
9 2VJX Ki = 11 uM IFL C6 H11 N O4 C1C(C(C(C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: M2F; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 NFG 1 1
2 M2F 1 1
3 DCB 0.702703 0.983871
4 NIN MBF BMA BMA 0.658228 0.983871
5 KHP 0.463768 0.777778
6 145 0.44 0.868852
7 PNW 0.424658 0.836066
8 147 0.424658 0.836066
9 PNG 0.424658 0.836066
10 GAL NPO 0.424658 0.836066
11 PNJ 0.407895 0.828125
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VOT; Ligand: NHV; Similar sites found: 61
This union binding pocket(no: 1) in the query (biounit: 2vot.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 2E40 LGC 0.000166 0.50736
2 2E40 LGC 0.0001907 0.50427
3 1UZ4 IFL 0.0003602 0.48948
4 2CER PGI 0.001084 0.46424
5 2CER PGI 0.00117 0.46265
6 4PTX BGC 0.000414 0.4602
7 2E9L BGC 0.002188 0.45978
8 4PTX BGC 0.0004627 0.45803
9 1PX8 XYP 0.0000642 0.45353
10 3PTQ NFG 0.0006648 0.45094
11 3GNP SOG 0.0007913 0.44754
12 3LPF Z77 0.001912 0.44275
13 1KWK GAL 0.002919 0.4416
14 4PBG BGP 0.000397 0.44106
15 4PBG BGP 0.0003966 0.44085
16 3PTQ NFG 0.0007572 0.44076
17 3AI0 PNW 0.001455 0.43562
18 1V08 NTZ 0.002291 0.43535
19 2O9R TCB 0.002508 0.42728
20 4CU7 GIF 0.001941 0.42292
21 4I4S LAT 0.01054 0.42216
22 4I4S LAT 0.01054 0.42216
23 4M82 NGB 0.004481 0.42187
24 2VRQ XYP XYP AHR 0.003348 0.42158
25 2X05 X05 0.002602 0.42098
26 2X05 X05 0.003321 0.41947
27 2E9L OLA 0.0162 0.41675
28 2WW2 SWA 0.006939 0.416
29 2E9L PLM 0.01614 0.41582
30 4CD6 IFM BMA 0.01039 0.41402
31 4D1J DGJ 0.001299 0.41361
32 4D1J DGJ 0.001387 0.41264
33 2NSX IFM 0.005745 0.41093
34 2NSX IFM 0.005745 0.41093
35 2NSX IFM 0.005745 0.41093
36 2NSX IFM 0.005745 0.41093
37 2NSX IFM 0.004395 0.4093
38 2NSX IFM 0.004395 0.4093
39 3F5K CE5 0.0006805 0.40721
40 1L1Y BGC BGC 0.01433 0.4071
41 2JEQ GAL BGC BGC BGC XYS BGC XYS 0.00434 0.40707
42 3S7O LBV 0.01898 0.40688
43 3F5K CE5 0.0007099 0.40671
44 3F5K CE5 0.0007099 0.40671
45 4D1J DGJ 0.0006222 0.40497
46 3TTY GLA 0.01318 0.40434
47 3CMJ SRT 0.0004486 0.4035
48 4D1J DGJ 0.0006989 0.40266
49 4D1J DGJ 0.0007076 0.40246
50 2CET PGI 0.0007287 0.40242
51 4D1J DGJ 0.0007196 0.4023
52 4D1J DGJ 0.0007281 0.40209
53 4D1J DGJ 0.0007388 0.40195
54 4D1J DGJ 0.0007484 0.40183
55 4D1J DGJ 0.000768 0.40143
56 3AYS CT3 0.004023 0.40127
57 3AYS CT3 0.0052 0.40127
58 2WVZ KIF 0.01051 0.40073
59 1W9D SEH 0.001096 0.40043
60 1WHT BZS 0.02049 0.40007
61 1WHT BZS 0.02049 0.40007
Pocket No.: 2; Query (leader) PDB : 2VOT; Ligand: NHV; Similar sites found: 59
This union binding pocket(no: 2) in the query (biounit: 2vot.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 2E40 LGC 0.0001928 0.50403
2 2E40 LGC 0.000223 0.50077
3 1UZ4 IFL 0.0003289 0.49174
4 4CD6 IFM BMA 0.0006701 0.4735
5 4PTX BGC 0.0004326 0.45934
6 4PTX BGC 0.0004547 0.45837
7 2CER PGI 0.001455 0.45811
8 2CER PGI 0.001599 0.45615
9 2E9L BGC 0.002926 0.45354
10 1PX8 XYP 0.00007167 0.45318
11 3PTQ NFG 0.0008263 0.44669
12 3LPF Z77 0.001961 0.44224
13 3GNP SOG 0.001048 0.44205
14 4PBG BGP 0.0004351 0.43946
15 4PBG BGP 0.0004375 0.4394
16 1KWK GAL 0.003573 0.43722
17 2X05 X05 0.001359 0.43695
18 3PTQ NFG 0.001138 0.43295
19 1V08 NTZ 0.002777 0.43149
20 3AI0 PNW 0.002276 0.42687
21 2O9R TCB 0.003001 0.42374
22 1QM5 GLC GLC GLC PO4 SGC GLC 0.01007 0.42264
23 2VRQ XYP XYP AHR 0.003216 0.42238
24 2X05 X05 0.003096 0.41766
25 2WW2 SWA 0.007328 0.41556
26 4CU7 GIF 0.003072 0.41368
27 4D1J DGJ 0.001445 0.41152
28 1QW9 KHP 0.005096 0.41109
29 2E9L OLA 0.02124 0.4109
30 4D1J DGJ 0.001537 0.41063
31 4M82 NGB 0.008092 0.40999
32 2E9L PLM 0.02117 0.40998
33 3E8T UQ8 0.03998 0.40903
34 1Q23 FUA 0.008505 0.40899
35 3TTY GLA 0.01164 0.40698
36 2JEQ GAL BGC BGC BGC XYS BGC XYS 0.004528 0.40652
37 1Q23 FUA 0.009106 0.40578
38 2WL9 MBD 0.0174 0.40473
39 2NSX IFM 0.005988 0.40343
40 2NSX IFM 0.005988 0.40343
41 4D1J DGJ 0.0007189 0.4031
42 4D1J DGJ 0.0007327 0.40288
43 3AYS CT3 0.003949 0.40236
44 3AYS CT3 0.005034 0.40236
45 1MAI I3P 0.01593 0.40235
46 3F5K CE5 0.0009023 0.40225
47 4D1J DGJ 0.0007296 0.4021
48 4D1J DGJ 0.0007516 0.40177
49 3TTY GLA 0.01493 0.40169
50 3TTY GLA 0.01493 0.40169
51 4D1J DGJ 0.0007731 0.40151
52 4D1J DGJ 0.0007735 0.40143
53 4D1J DGJ 0.0007809 0.40127
54 3PQB VGP 0.01362 0.4012
55 3PQB VGP 0.01373 0.40104
56 4D1J DGJ 0.0008005 0.40098
57 2WVZ KIF 0.01076 0.40026
58 3CMJ SRT 0.0005798 0.40024
59 3UG4 AHR 0.0007313 0.40015
Feedback