Receptor
PDB id Resolution Class Description Source Keywords
5EYY 1.9 Å NON-ENZYME: BINDING TETRAGONAL FORM OF CENTROLOBIUM TOMENTOSUM SEED LECTIN (CTL) WITH MAN1-3MAN-OME. CENTROLOBIUM TOMENTOSUM LECTIN CENTROLOBIUM TOMENTOSUM DALBERGIEAE CTL METHYL DIMANNOSIDE. SUGAR BINDING PROTEIN
Ref.: STRUCTURAL ANALYSIS OF CENTROLOBIUM TOMENTOSUM SEED WITH INFLAMMATORY ACTIVITY. ARCH.BIOCHEM.BIOPHYS. V. 596 73 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MDM A:304;
Valid;
none;
submit data
356.323 C13 H24 O11 CO[C@...
CA A:302;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
NAG A:301;
Invalid;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
MN A:303;
Part of Protein;
none;
submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5EYY 1.9 Å NON-ENZYME: BINDING TETRAGONAL FORM OF CENTROLOBIUM TOMENTOSUM SEED LECTIN (CTL) WITH MAN1-3MAN-OME. CENTROLOBIUM TOMENTOSUM LECTIN CENTROLOBIUM TOMENTOSUM DALBERGIEAE CTL METHYL DIMANNOSIDE. SUGAR BINDING PROTEIN
Ref.: STRUCTURAL ANALYSIS OF CENTROLOBIUM TOMENTOSUM SEED WITH INFLAMMATORY ACTIVITY. ARCH.BIOCHEM.BIOPHYS. V. 596 73 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 510 families.
1 5EYX - MDM C13 H24 O11 CO[C@@H]1[....
2 5EYY - MDM C13 H24 O11 CO[C@@H]1[....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 391 families.
1 1S1A - MAN MMA n/a n/a
2 2ARB Ka = 26000 M^-1 NAG MAN n/a n/a
3 1N3Q - GLC BDF n/a n/a
4 2AR6 Ka = 63000 M^-1 NAG MAN MAN MAN NAG n/a n/a
5 1N3O - GYP C7 H14 O6 CO[C@@H]1[....
6 1N3P - GLC FRU n/a n/a
7 2ARX - MAN MAN n/a n/a
8 2ARE Ka = 1900 M^-1 MAN C6 H12 O6 C([C@@H]1[....
9 3ZYR Kd = 4.6 uM ASN NAG NAG BMA MAN MAN NAG NAG n/a n/a
10 3ZVX - MAN MAN MAN n/a n/a
11 5U38 - MDM C13 H24 O11 CO[C@@H]1[....
12 5EYX - MDM C13 H24 O11 CO[C@@H]1[....
13 5EYY - MDM C13 H24 O11 CO[C@@H]1[....
50% Homology Family (61)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 298 families.
1 5T55 Kd = 0.68 nM NGA GLA GAL BGC n/a n/a
2 5T54 Kd = 0.87 nM A2G GLA FUC n/a n/a
3 5T5J Kd = 0.73 nM ACA SER SER VAL GLY A2G n/a n/a
4 5T52 Kd = 0.54 nM NGA C8 H15 N O6 CC(=O)N[C@....
5 5T5L Kd = 0.73 nM ACE SER SER VAL GLY A2G n/a n/a
6 5T5P Kd = 0.71 nM ACE SER THR VAL GLY A2G n/a n/a
7 1FNZ - A2G C8 H15 N O6 CC(=O)N[C@....
8 1S1A - MAN MMA n/a n/a
9 2ARB Ka = 26000 M^-1 NAG MAN n/a n/a
10 1N3Q - GLC BDF n/a n/a
11 2AR6 Ka = 63000 M^-1 NAG MAN MAN MAN NAG n/a n/a
12 1N3O - GYP C7 H14 O6 CO[C@@H]1[....
13 1N3P - GLC FRU n/a n/a
14 2ARX - MAN MAN n/a n/a
15 2ARE Ka = 1900 M^-1 MAN C6 H12 O6 C([C@@H]1[....
16 1LED - FUC GAL MAG FUC n/a n/a
17 1GSL - FUC GAL MAG FUC n/a n/a
18 1V00 - LAT C12 H22 O11 C([C@@H]1[....
19 3N3H - CIT C6 H8 O7 C(C(=O)O)C....
20 3N36 - GLA C6 H12 O6 C([C@@H]1[....
21 1AX0 Ka = 1340 M^-1 A2G C8 H15 N O6 CC(=O)N[C@....
22 1UZY - GAL BGC n/a n/a
23 1LTE - BGC GAL n/a n/a
24 1AX1 Ka = 1940 M^-1 BGC GAL n/a n/a
25 1AX2 Ka = 9730 M^-1 NDG GAL n/a n/a
26 1GZC Kd = 0.32 mM LAT C12 H22 O11 C([C@@H]1[....
27 3N35 - A2G C8 H15 N O6 CC(=O)N[C@....
28 1AXZ Ka = 1570 M^-1 GAL C6 H12 O6 C([C@@H]1[....
29 1GZ9 Kd = 0.31 mM FUC LAT n/a n/a
30 3ZYR Kd = 4.6 uM ASN NAG NAG BMA MAN MAN NAG NAG n/a n/a
31 3ZVX - MAN MAN MAN n/a n/a
32 5U38 - MDM C13 H24 O11 CO[C@@H]1[....
33 5KXE Kd = 5.45 uM 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
34 5KXB - NGA C8 H15 N O6 CC(=O)N[C@....
35 5KXC - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
36 5KXD - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
37 4WV8 - LBT C12 H22 O11 C([C@@H]1[....
38 4U2A - A2G C8 H15 N O6 CC(=O)N[C@....
39 4U36 - TNR C11 H20 N2 O8 CC(=O)N[C@....
40 1JXN - MFU C7 H14 O5 C[C@H]1[C@....
41 3WCS - MAN NAG GAL n/a n/a
42 3WOG - MAN NAG n/a n/a
43 5EYX - MDM C13 H24 O11 CO[C@@H]1[....
44 5EYY - MDM C13 H24 O11 CO[C@@H]1[....
45 2BQP - GLC C6 H12 O6 C([C@@H]1[....
46 5T7P - XMM C14 H15 Br Cl N O6 c1cc(c(c2c....
47 2DVA - GAL MGC n/a n/a
48 2DV9 - GAL GAL n/a n/a
49 1V6K - GAL GLC n/a n/a
50 1V6L - GAL BGC n/a n/a
51 2DVD - GAL GAL n/a n/a
52 2TEP - GAL NGA n/a n/a
53 2DVB - GAL C6 H12 O6 C([C@@H]1[....
54 1V6I - GAL GLC n/a n/a
55 2PEL Ki = 1.37 mM LAT C12 H22 O11 C([C@@H]1[....
56 1G9F - GAL NAG GAL NAG GAL n/a n/a
57 2DTW - 2GS C7 H14 O6 CO[C@@H]1[....
58 1WBL - AMG C7 H14 O6 CO[C@@H]1[....
59 2ZMK - GLA EGA n/a n/a
60 2D3S - TNR C11 H20 N2 O8 CC(=O)N[C@....
61 2FMD - MAN MAN n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MDM; Similar ligands found: 191
No: Ligand ECFP6 Tc MDL keys Tc
1 M13 1 1
2 GAL MBG 1 1
3 MDM 1 1
4 MAN MMA MAN 0.696429 1
5 GLC BGC BGC BGC BGC BGC BGC 0.641509 0.942857
6 BGC BGC BGC GLC BGC BGC 0.641509 0.942857
7 GLA MBG 0.62 1
8 WZ3 0.619048 0.972222
9 BQZ 0.617021 0.857143
10 MMA MAN 0.615385 1
11 DR5 0.615385 1
12 MMA 0.613636 0.914286
13 AMG 0.613636 0.914286
14 MBG 0.613636 0.914286
15 GYP 0.613636 0.914286
16 LB2 0.607843 0.942857
17 M3M 0.607843 0.942857
18 MAN GLC 0.607843 0.942857
19 NGR 0.607843 0.942857
20 GLA GAL GAL 0.596491 0.942857
21 TRE 0.590909 0.942857
22 NAG MBG 0.583333 0.744681
23 MAN MAN MAN GLC 0.57377 0.942857
24 XLM 0.561404 0.972222
25 GAL MGC 0.559322 0.744681
26 BGC BGC BGC BGC BGC BGC BGC BGC 0.557377 0.942857
27 NAG BMA MAN MAN MAN MAN MAN 0.549296 0.921053
28 MAN BMA NAG 0.530303 0.73913
29 GLA GAL NAG 0.530303 0.73913
30 2M4 0.528302 0.942857
31 LAT GLA 0.528302 0.942857
32 NAG MAN MMA 0.507246 0.744681
33 OPM MAN MAN 0.492754 0.809524
34 P3M 0.492308 0.733333
35 BMA BMA 0.491228 0.864865
36 BGC BGC 0.491228 0.864865
37 DOM 0.491228 0.891892
38 LBT 0.490909 0.942857
39 LAT 0.490909 0.942857
40 GLC GAL 0.490909 0.942857
41 BMA GAL 0.490909 0.942857
42 CBI 0.490909 0.942857
43 GLA GLA 0.490909 0.942857
44 BGC BMA 0.490909 0.942857
45 GAL BGC 0.490909 0.942857
46 MAB 0.490909 0.942857
47 N9S 0.490909 0.942857
48 B2G 0.490909 0.942857
49 CBK 0.490909 0.942857
50 MAL 0.490909 0.942857
51 GLA GAL 0.490909 0.942857
52 BGC GAL 0.490909 0.942857
53 GLA MMA ABE 0.485294 0.921053
54 MAN MAN BMA MAN 0.484848 0.942857
55 MAN MAN MAN MAN 0.484848 0.942857
56 BMA MAN MAN MAN 0.483871 0.942857
57 GAL FUC 0.482759 0.942857
58 BGC BGC ZZ1 0.48 0.772727
59 4MU MAN MAN 0.48 0.772727
60 MAN BMA MAN MAN MAN 0.477612 0.942857
61 M5S 0.477612 0.942857
62 MAN BMA MAN 0.47619 0.942857
63 CGC 0.47541 0.888889
64 GLA EGA 0.474576 0.944444
65 RZM 0.473684 0.659574
66 GLA GAL FUC 0.46875 0.971429
67 FUC GLA GLA 0.46875 0.971429
68 GLA GLA FUC 0.46875 0.971429
69 GAL GAL FUC 0.46875 0.971429
70 FUC GAL GLA 0.46875 0.971429
71 IFM BGC 0.466667 0.680851
72 IFM BMA 0.466667 0.680851
73 BMA BMA MAN 0.466667 0.942857
74 MAN MAN BMA 0.466667 0.942857
75 BMA IFM 0.466667 0.680851
76 GTM BGC BGC 0.463768 0.921053
77 GAL GAL SO4 0.461538 0.634615
78 A2G GAL 0.460317 0.73913
79 GAL NGA 0.460317 0.73913
80 GAL A2G 0.460317 0.73913
81 BGC GAL NAG GAL 0.459459 0.73913
82 GAL NAG GAL GLC 0.459459 0.73913
83 GLC DMJ 0.459016 0.666667
84 GLA GAL BGC 0.457627 0.942857
85 GLC BGC BGC BGC BGC 0.457627 0.942857
86 CE8 0.457627 0.942857
87 MAN MAN BMA BMA BMA BMA 0.457627 0.942857
88 BGC GLC GLC GLC GLC 0.457627 0.942857
89 BGC GLC GLC 0.457627 0.942857
90 BGC BGC BGC BGC BGC 0.457627 0.942857
91 DXI 0.457627 0.942857
92 BMA MAN BMA 0.457627 0.942857
93 MAN BMA BMA BMA BMA 0.457627 0.942857
94 GLC BGC GLC 0.457627 0.942857
95 CE6 0.457627 0.942857
96 BMA BMA BMA BMA BMA 0.457627 0.942857
97 MAN BMA BMA 0.457627 0.942857
98 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.457627 0.942857
99 MLR 0.457627 0.942857
100 MT7 0.457627 0.942857
101 BGC BGC BGC BGC 0.457627 0.942857
102 GAL GAL GAL 0.457627 0.942857
103 U63 0.457627 0.846154
104 B4G 0.457627 0.942857
105 GLC BGC BGC 0.457627 0.942857
106 BGC GLC GLC GLC GLC GLC GLC 0.457627 0.942857
107 GLC GLC BGC 0.457627 0.942857
108 CTT 0.457627 0.942857
109 BMA BMA BMA BMA BMA BMA 0.457627 0.942857
110 GLC BGC BGC BGC BGC BGC 0.457627 0.942857
111 GLC GAL GAL 0.457627 0.942857
112 BGC BGC BGC GLC 0.457627 0.942857
113 GLC GLC GLC GLC GLC 0.457627 0.942857
114 BGC BGC GLC 0.457627 0.942857
115 BGC BGC BGC 0.457627 0.942857
116 CEX 0.457627 0.942857
117 GLC BGC BGC BGC 0.457627 0.942857
118 CEY 0.457627 0.942857
119 CTR 0.457627 0.942857
120 MAN BMA BMA BMA BMA BMA 0.457627 0.942857
121 BGC GLC GLC GLC 0.457627 0.942857
122 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.457627 0.942857
123 CE5 0.457627 0.942857
124 MTT 0.457627 0.942857
125 GLA GAL GLC 0.457627 0.942857
126 CT3 0.457627 0.942857
127 BMA BMA BMA 0.457627 0.942857
128 BGC BGC BGC BGC BGC BGC 0.457627 0.942857
129 NAG GAL GAL NAG GAL 0.453333 0.693878
130 NAG GAL GAL NAG 0.453333 0.693878
131 GAL NAG GAL NAG GAL NAG 0.453333 0.68
132 BMA FRU 0.45 0.8
133 5QP 0.45 0.837838
134 FRU GAL 0.45 0.8
135 MAN MMA 0.448276 1
136 T6P 0.448276 0.733333
137 GLC GAL NAG GAL 0.447368 0.73913
138 LAT NAG GAL 0.447368 0.73913
139 MAL EDO 0.442623 0.891892
140 BGC OXZ 0.442623 0.64
141 9MR 0.442623 0.711111
142 MAN 7D1 0.440678 0.842105
143 MAN MAN MAN BMA MAN 0.438356 0.942857
144 MGL SGC GLC GLC 0.438356 0.921053
145 MGL SGC BGC BGC 0.438356 0.921053
146 BGC BGC SGC MGL 0.438356 0.921053
147 GLA GAL BGC 5VQ 0.4375 0.894737
148 NDG GAL 0.4375 0.73913
149 GAL NDG 0.4375 0.73913
150 NLC 0.4375 0.73913
151 8VZ 0.4375 0.68
152 GAL NGA GLA BGC GAL 0.435897 0.73913
153 FMO 0.435484 0.825
154 MAN MNM 0.435484 0.673469
155 NOY BGC 0.435484 0.673469
156 NOJ GLC 0.435484 0.666667
157 MAG FUC GAL 0.430556 0.729167
158 GAL NAG GAL BGC 0.43038 0.708333
159 ABL 0.428571 0.673469
160 MVP 0.428571 0.702128
161 NAG NAG BMA MAN 0.426829 0.641509
162 NGT GAL 0.426471 0.666667
163 GAL NGT 0.426471 0.666667
164 MAN DGO 0.42623 0.864865
165 GLA MAN ABE 0.422535 0.918919
166 MAN G63 0.421875 0.627451
167 GDQ GLC 0.421875 0.64
168 MAN MAN MAN BMA MAN MAN MAN 0.419753 1
169 FUC BGC GAL 0.41791 0.971429
170 GLA GAL GLC NBU 0.41791 0.85
171 NAG BMA 0.41791 0.66
172 4RS 0.415385 0.829268
173 NAG GAL BGC 0.413333 0.73913
174 WZ5 0.406977 0.744681
175 GLC 7LQ 0.40625 0.837838
176 DMU 0.405797 0.790698
177 LMT 0.405797 0.790698
178 GLC GLC XYP 0.405797 0.942857
179 UMQ 0.405797 0.790698
180 LMU 0.405797 0.790698
181 A2G SER GAL 0.405405 0.653846
182 GAL TNR 0.405405 0.653846
183 NGA SER GAL 0.405405 0.653846
184 GAL SER A2G 0.405405 0.653846
185 NGA GLA GAL BGC 0.405063 0.73913
186 TUR 0.403226 0.8
187 BTU 0.403226 0.8
188 GLC FRU 0.403226 0.8
189 BGC GLA GAL FUC 0.4 0.971429
190 NAG BMA MAN MAN MAN MAN 0.4 0.73913
191 SOR GLC GLC 0.4 0.916667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5EYY; Ligand: MDM; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 5eyy.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 2GUC MAN 6.55738
2 2GUD MAN 6.55738
Pocket No.: 2; Query (leader) PDB : 5EYY; Ligand: MDM; 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: 5eyy.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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