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 C1[C@@H]([....
2 2VR4 Ki = 2.1 uM 17B C10 H21 N3 O4 C(CC/N=C1/....
3 2VO5 Ki = 13 uM VBZ C15 H21 N O4 c1ccc(cc1)....
4 2VOT Ki = 72 nM NHV C15 H20 N3 O4 c1ccc(cc1)....
5 2WBK - M2F C12 H13 F N2 O9 c1cc(c(cc1....
6 2VJX Ki = 11 uM IFL C6 H11 N O4 C1[C@@H]([....
7 2VQT Ki = 1 uM 15A C8 H17 N3 O4 C(C/N=C1/[....
8 2VL4 Ki = 975 nM MNM C6 H13 N O4 C1[C@@H]([....
9 2VMF Ki = 1400 nM MVL C8 H12 N2 O4 c1cn2c(n1)....
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 C1[C@@H]([....
2 2VR4 Ki = 2.1 uM 17B C10 H21 N3 O4 C(CC/N=C1/....
3 2VO5 Ki = 13 uM VBZ C15 H21 N O4 c1ccc(cc1)....
4 2VOT Ki = 72 nM NHV C15 H20 N3 O4 c1ccc(cc1)....
5 2WBK - M2F C12 H13 F N2 O9 c1cc(c(cc1....
6 2VJX Ki = 11 uM IFL C6 H11 N O4 C1[C@@H]([....
7 2VQT Ki = 1 uM 15A C8 H17 N3 O4 C(C/N=C1/[....
8 2VL4 Ki = 975 nM MNM C6 H13 N O4 C1[C@@H]([....
9 2VMF Ki = 1400 nM MVL C8 H12 N2 O4 c1cn2c(n1)....
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 C1[C@@H]([....
2 2VR4 Ki = 2.1 uM 17B C10 H21 N3 O4 C(CC/N=C1/....
3 2VO5 Ki = 13 uM VBZ C15 H21 N O4 c1ccc(cc1)....
4 2VOT Ki = 72 nM NHV C15 H20 N3 O4 c1ccc(cc1)....
5 2WBK - M2F C12 H13 F N2 O9 c1cc(c(cc1....
6 2VJX Ki = 11 uM IFL C6 H11 N O4 C1[C@@H]([....
7 2VQT Ki = 1 uM 15A C8 H17 N3 O4 C(C/N=C1/[....
8 2VL4 Ki = 975 nM MNM C6 H13 N O4 C1[C@@H]([....
9 2VMF Ki = 1400 nM MVL C8 H12 N2 O4 c1cn2c(n1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: M2F; Similar ligands found: 15
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
7 147 0.424658 0.836066
8 MBE 0.424658 0.836066
9 GLA NPO 0.424658 0.836066
10 NBZ GLA 0.424658 0.836066
11 PNW 0.424658 0.836066
12 PNA 0.424658 0.836066
13 PNG 0.424658 0.836066
14 GAL NPO 0.424658 0.836066
15 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: 51
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 5GNX BGC 0.0001565 0.50825
2 2E40 LGC 0.000166 0.50736
3 2E40 LGC 0.0001907 0.50427
4 1UZ4 IFL 0.0003602 0.48948
5 4PTX BGC 0.000414 0.4602
6 2E9L BGC 0.002188 0.45978
7 4PTX BGC 0.0004627 0.45803
8 1PX8 XYP 0.0000642 0.45353
9 3PTQ NFG 0.0006648 0.45094
10 3GNP SOG 0.0007913 0.44754
11 1KWK GAL 0.002919 0.4416
12 4PBG BGP 0.000397 0.44106
13 4PBG BGP 0.0003966 0.44085
14 3PTQ NFG 0.0007572 0.44076
15 3AI0 PNW 0.001455 0.43562
16 2O9R TCB 0.002508 0.42728
17 4CU7 GIF 0.001941 0.42292
18 4M82 NGB 0.004481 0.42187
19 2VRQ XYP XYP AHR 0.003348 0.42158
20 2X05 X05 0.002602 0.42098
21 2X05 X05 0.003321 0.41947
22 2E9L OLA 0.0162 0.41675
23 2WW2 SWA 0.006939 0.416
24 2E9L PLM 0.01614 0.41582
25 4CD6 IFM BMA 0.01039 0.41402
26 4D1J DGJ 0.001299 0.41361
27 4D1J DGJ 0.001387 0.41264
28 2NSX IFM 0.005745 0.41093
29 2NSX IFM 0.005745 0.41093
30 2NSX IFM 0.005745 0.41093
31 2NSX IFM 0.005745 0.41093
32 2NSX IFM 0.004395 0.4093
33 2NSX IFM 0.004395 0.4093
34 2JEQ GAL BGC BGC BGC XYS BGC XYS 0.00434 0.40707
35 3S7O LBV 0.01898 0.40688
36 4D1J DGJ 0.0006222 0.40497
37 3TTY GLA 0.01318 0.40434
38 3CMJ SRT 0.0004486 0.4035
39 4D1J DGJ 0.0006989 0.40266
40 4D1J DGJ 0.0007076 0.40246
41 4D1J DGJ 0.0007196 0.4023
42 4D1J DGJ 0.0007281 0.40209
43 4D1J DGJ 0.0007388 0.40195
44 4D1J DGJ 0.0007484 0.40183
45 4D1J DGJ 0.000768 0.40143
46 3AYS CT3 0.0052 0.40127
47 3AYS CT3 0.004023 0.40127
48 2WVZ KIF 0.01051 0.40073
49 1W9D SEH 0.001096 0.40043
50 1WHT BZS 0.02049 0.40007
51 1WHT BZS 0.02049 0.40007
Pocket No.: 2; Query (leader) PDB : 2VOT; Ligand: NHV; Similar sites found: 55
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 5GNX BGC 0.0001732 0.50596
2 2E40 LGC 0.0001928 0.50403
3 2E40 LGC 0.000223 0.50077
4 1UZ4 IFL 0.0003289 0.49174
5 4CD6 IFM BMA 0.0006701 0.4735
6 4PTX BGC 0.0004326 0.45934
7 4PTX BGC 0.0004547 0.45837
8 2E9L BGC 0.002926 0.45354
9 1PX8 XYP 0.00007167 0.45318
10 3PTQ NFG 0.0008263 0.44669
11 3GNP SOG 0.001048 0.44205
12 4PBG BGP 0.0004351 0.43946
13 4PBG BGP 0.0004375 0.4394
14 1KWK GAL 0.003573 0.43722
15 2X05 X05 0.001359 0.43695
16 3PTQ NFG 0.001138 0.43295
17 3AI0 PNW 0.002276 0.42687
18 2O9R TCB 0.003001 0.42374
19 1QM5 GLC GLC GLC PO4 SGC GLC 0.01007 0.42264
20 2VRQ XYP XYP AHR 0.003216 0.42238
21 2X05 X05 0.003096 0.41766
22 2WW2 SWA 0.007328 0.41556
23 4CU7 GIF 0.003072 0.41368
24 4D1J DGJ 0.001445 0.41152
25 1QW9 KHP 0.005096 0.41109
26 2E9L OLA 0.02124 0.4109
27 4D1J DGJ 0.001537 0.41063
28 4M82 NGB 0.008092 0.40999
29 2E9L PLM 0.02117 0.40998
30 3E8T UQ8 0.03998 0.40903
31 1Q23 FUA 0.008505 0.40899
32 3TTY GLA 0.01164 0.40698
33 2JEQ GAL BGC BGC BGC XYS BGC XYS 0.004528 0.40652
34 1Q23 FUA 0.009106 0.40578
35 2WL9 MBD 0.0174 0.40473
36 2NSX IFM 0.005988 0.40343
37 2NSX IFM 0.005988 0.40343
38 4D1J DGJ 0.0007189 0.4031
39 4D1J DGJ 0.0007327 0.40288
40 3AYS CT3 0.005034 0.40236
41 3AYS CT3 0.003949 0.40236
42 1MAI I3P 0.01593 0.40235
43 4D1J DGJ 0.0007296 0.4021
44 4D1J DGJ 0.0007516 0.40177
45 3TTY GLA 0.01493 0.40169
46 3TTY GLA 0.01493 0.40169
47 4D1J DGJ 0.0007731 0.40151
48 4D1J DGJ 0.0007735 0.40143
49 4D1J DGJ 0.0007809 0.40127
50 3PQB VGP 0.01362 0.4012
51 3PQB VGP 0.01373 0.40104
52 4D1J DGJ 0.0008005 0.40098
53 2WVZ KIF 0.01076 0.40026
54 3CMJ SRT 0.0005798 0.40024
55 3UG4 AHR 0.0007313 0.40015
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