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 544 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 420 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 319 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: 201
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL MBG 1 1
2 M13 1 1
3 MDM 1 1
4 MAN MMA 1 1
5 MAN MMA MAN 0.696429 1
6 BGC BGC BGC BGC BGC BGC 0.641509 0.942857
7 GLC BGC BGC BGC BGC BGC BGC 0.641509 0.942857
8 GLC GLC GLC 0.641509 0.942857
9 GLC GLC BGC 0.641509 0.942857
10 GLC GLC GLC GLC 0.641509 0.942857
11 BGC BGC BGC GLC BGC BGC 0.641509 0.942857
12 GLA MBG 0.62 1
13 WZ3 0.619048 0.972222
14 BQZ 0.617021 0.857143
15 MMA MAN 0.615385 1
16 DR5 0.615385 1
17 AMG 0.613636 0.914286
18 MBG 0.613636 0.914286
19 GYP 0.613636 0.914286
20 MMA 0.613636 0.914286
21 GLC GLC 0.607843 0.942857
22 M3M 0.607843 0.942857
23 LB2 0.607843 0.942857
24 GLA GAL 0.607843 0.942857
25 GLC BGC 0.607843 0.942857
26 NGR 0.607843 0.942857
27 GLA GLA 0.607843 0.942857
28 MAN GLC 0.607843 0.942857
29 GLA GAL GAL 0.596491 0.942857
30 TRE 0.590909 0.942857
31 NAG MBG 0.583333 0.744681
32 MAN MAN MAN GLC 0.57377 0.942857
33 XLM 0.561404 0.972222
34 GAL MGC 0.559322 0.744681
35 BGC BGC BGC BGC BGC BGC BGC BGC 0.557377 0.942857
36 MAN BMA NAG 0.530303 0.73913
37 GLA GAL NAG 0.530303 0.73913
38 2M4 0.528302 0.942857
39 LAT GLA 0.528302 0.942857
40 BMA MAN 0.528302 0.942857
41 BGC GLC 0.528302 0.942857
42 NAG MAN MMA 0.507246 0.744681
43 OPM MAN MAN 0.492754 0.809524
44 P3M 0.492308 0.733333
45 DOM 0.491228 0.891892
46 BGC BGC 0.491228 0.864865
47 GAL BGC 0.490909 0.942857
48 MAB 0.490909 0.942857
49 BMA BMA 0.490909 0.942857
50 B2G 0.490909 0.942857
51 BMA GAL 0.490909 0.942857
52 LBT 0.490909 0.942857
53 CBK 0.490909 0.942857
54 CBI 0.490909 0.942857
55 BGC BMA 0.490909 0.942857
56 MAL 0.490909 0.942857
57 N9S 0.490909 0.942857
58 LAT 0.490909 0.942857
59 GLC GAL 0.490909 0.942857
60 BGC GAL 0.490909 0.942857
61 GLA MMA ABE 0.485294 0.921053
62 MAN MAN MAN MAN 0.484848 0.942857
63 MAN MAN BMA MAN 0.484848 0.942857
64 BMA MAN MAN MAN 0.483871 0.942857
65 GAL FUC 0.482759 0.942857
66 BGC BGC ZZ1 0.48 0.772727
67 4MU MAN MAN 0.48 0.772727
68 M5S 0.477612 0.942857
69 MAN BMA MAN MAN MAN 0.477612 0.942857
70 MAN MAN MAN 0.47619 0.942857
71 MAN BMA MAN 0.47619 0.942857
72 CGC 0.47541 0.888889
73 GLA EGA 0.474576 0.944444
74 RZM 0.473684 0.659574
75 FUC GAL GLA 0.46875 0.971429
76 GLA GLA FUC 0.46875 0.971429
77 GLA GAL FUC 0.46875 0.971429
78 FUC GLA GLA 0.46875 0.971429
79 GAL GAL FUC 0.46875 0.971429
80 BMA IFM 0.466667 0.680851
81 IFM BGC 0.466667 0.680851
82 MAN MAN BMA 0.466667 0.942857
83 IFM BMA 0.466667 0.680851
84 BMA BMA MAN 0.466667 0.942857
85 GTM BGC BGC 0.463768 0.921053
86 GAL GAL SO4 0.461538 0.634615
87 NAG GAL 0.460317 0.73913
88 GAL NAG 0.460317 0.73913
89 GAL NGA 0.460317 0.73913
90 GAL A2G 0.460317 0.73913
91 BGC GAL NAG GAL 0.459459 0.73913
92 GAL NAG GAL GLC 0.459459 0.73913
93 BGC BGC BGC BGC BGC BGC BGC 0.459016 0.942857
94 GLC DMJ 0.459016 0.666667
95 BGC BGC BGC BGC BGC 0.459016 0.942857
96 GLC GLC GLC GLC GLC 0.457627 0.942857
97 MTT 0.457627 0.942857
98 MLR 0.457627 0.942857
99 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.457627 0.942857
100 MAN BMA BMA BMA BMA 0.457627 0.942857
101 BGC GLC GLC GLC GLC 0.457627 0.942857
102 BGC GLC GLC 0.457627 0.942857
103 GLC BGC GLC 0.457627 0.942857
104 GLC BGC BGC BGC 0.457627 0.942857
105 GLA GAL BGC 0.457627 0.942857
106 CE8 0.457627 0.942857
107 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.457627 0.942857
108 MAN BMA BMA 0.457627 0.942857
109 MAN MAN BMA BMA BMA BMA 0.457627 0.942857
110 BGC BGC BGC GLC 0.457627 0.942857
111 B4G 0.457627 0.942857
112 BMA BMA BMA BMA BMA BMA 0.457627 0.942857
113 MAN BMA BMA BMA BMA BMA 0.457627 0.942857
114 CTT 0.457627 0.942857
115 GLC GAL GAL 0.457627 0.942857
116 BGC GLC GLC GLC 0.457627 0.942857
117 BGC BGC BGC BGC 0.457627 0.942857
118 BGC BGC GLC 0.457627 0.942857
119 BMA BMA BMA BMA BMA 0.457627 0.942857
120 BMA MAN BMA 0.457627 0.942857
121 CE6 0.457627 0.942857
122 GLC BGC BGC BGC BGC BGC 0.457627 0.942857
123 U63 0.457627 0.846154
124 CT3 0.457627 0.942857
125 BGC GLC GLC GLC GLC GLC GLC 0.457627 0.942857
126 MT7 0.457627 0.942857
127 GLC BGC BGC BGC BGC 0.457627 0.942857
128 BGC BGC BGC 0.457627 0.942857
129 GAL GAL GAL 0.457627 0.942857
130 DXI 0.457627 0.942857
131 CTR 0.457627 0.942857
132 BMA BMA BMA 0.457627 0.942857
133 CEX 0.457627 0.942857
134 GLA GAL GLC 0.457627 0.942857
135 CEY 0.457627 0.942857
136 CE5 0.457627 0.942857
137 GLC BGC BGC 0.457627 0.942857
138 GAL NAG GAL NAG GAL NAG 0.453333 0.68
139 NAG GAL GAL NAG 0.453333 0.693878
140 NAG GAL GAL NAG GAL 0.453333 0.693878
141 W9T 0.45 0.8
142 FRU GAL 0.45 0.8
143 5QP 0.45 0.837838
144 BMA FRU 0.45 0.8
145 T6P 0.448276 0.733333
146 GLC GAL NAG GAL 0.447368 0.73913
147 LAT NAG GAL 0.447368 0.73913
148 MAL EDO 0.442623 0.891892
149 9MR 0.442623 0.711111
150 BGC OXZ 0.442623 0.64
151 MAN 7D1 0.440678 0.842105
152 A2G GAL 0.439394 0.66
153 MGL SGC GLC GLC 0.438356 0.921053
154 MAN MAN MAN BMA MAN 0.438356 0.942857
155 MGL SGC BGC BGC 0.438356 0.921053
156 BGC BGC SGC MGL 0.438356 0.921053
157 NLC 0.4375 0.73913
158 8VZ 0.4375 0.68
159 GLA GAL BGC 5VQ 0.4375 0.894737
160 GAL NDG 0.4375 0.73913
161 GAL NGA GLA BGC GAL 0.435897 0.73913
162 FMO 0.435484 0.825
163 MAN MNM 0.435484 0.673469
164 NOY BGC 0.435484 0.673469
165 NOJ GLC 0.435484 0.666667
166 MAG FUC GAL 0.430556 0.729167
167 GAL NAG GAL BGC 0.43038 0.708333
168 MVP 0.428571 0.702128
169 ABL 0.428571 0.673469
170 NAG NAG BMA MAN 0.426829 0.641509
171 GAL NGT 0.426471 0.666667
172 NGT GAL 0.426471 0.666667
173 MAN DGO 0.42623 0.864865
174 GLA MAN ABE 0.422535 0.918919
175 GDQ GLC 0.421875 0.64
176 MAN G63 0.421875 0.627451
177 MAN MAN MAN BMA MAN MAN MAN 0.419753 1
178 GLA GAL GLC NBU 0.41791 0.85
179 FUC BGC GAL 0.41791 0.971429
180 NAG BMA 0.41791 0.66
181 FUC GLC BGC GAL 0.41791 0.971429
182 4RS 0.415385 0.829268
183 NAG GAL BGC 0.413333 0.73913
184 WZ5 0.406977 0.744681
185 GLC 7LQ 0.40625 0.837838
186 LMU 0.405797 0.790698
187 GLC GLC XYP 0.405797 0.942857
188 UMQ 0.405797 0.790698
189 LMT 0.405797 0.790698
190 DMU 0.405797 0.790698
191 A2G SER GAL 0.405405 0.653846
192 NGA SER GAL 0.405405 0.653846
193 GAL TNR 0.405405 0.653846
194 GAL SER A2G 0.405405 0.653846
195 NGA GLA GAL BGC 0.405063 0.73913
196 TUR 0.403226 0.8
197 GLC FRU 0.403226 0.8
198 BTU 0.403226 0.8
199 BGC GLA GAL FUC 0.4 0.971429
200 NAG BMA MAN MAN MAN MAN 0.4 0.73913
201 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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