Receptor
PDB id Resolution Class Description Source Keywords
5EYX 2.25 Å NON-ENZYME: BINDING MONOCLINIC FORM OF CENTROLOBIUM TOMENTOSUM SEED LECTIN (CTL) WITH MAN1-3MAN-OME. CENTROLOBIUM TOMENTOSUM LECTIN CENTROLOBIUM TOMENTOSUM DALBERGIEAE METHYL DIMANNOCTL 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
CA A:301;
B:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
NAG B:303;
A:303;
Invalid;
Invalid;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
MDM A:304;
B:304;
Valid;
Valid;
none;
none;
submit data
356.323 C13 H24 O11 CO[C@...
MN B:302;
A:302;
Part of Protein;
Part of Protein;
none;
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 473 families.
1 5EYX - MDM C13 H24 O11 CO[C@@H]1[....
2 5EYY - MDM C13 H24 O11 CO[C@@H]1[....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 355 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 5EYX - MDM C13 H24 O11 CO[C@@H]1[....
12 5EYY - MDM C13 H24 O11 CO[C@@H]1[....
50% Homology Family (59)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 5T54 Kd = 0.87 nM A2G GLA FUC n/a n/a
2 5T5J Kd = 0.73 nM ACA SER SER VAL GLY A2G n/a n/a
3 5T52 Kd = 0.54 nM NGA C8 H15 N O6 CC(=O)N[C@....
4 5T5L Kd = 0.73 nM ACE SER SER VAL GLY A2G n/a n/a
5 5T5P Kd = 0.71 nM ACE SER THR VAL GLY A2G n/a n/a
6 1FNZ - A2G C8 H15 N O6 CC(=O)N[C@....
7 1S1A - MAN MMA n/a n/a
8 2ARB Ka = 26000 M^-1 NAG MAN n/a n/a
9 1N3Q - GLC BDF n/a n/a
10 2AR6 Ka = 63000 M^-1 NAG MAN MAN MAN NAG n/a n/a
11 1N3O - GYP C7 H14 O6 CO[C@@H]1[....
12 1N3P - GLC FRU n/a n/a
13 2ARX - MAN MAN n/a n/a
14 2ARE Ka = 1900 M^-1 MAN C6 H12 O6 C([C@@H]1[....
15 1LED - FUC GAL MAG FUC n/a n/a
16 1GSL - FUC GAL MAG FUC n/a n/a
17 1V00 - LAT C12 H22 O11 C([C@@H]1[....
18 3N3H - CIT C6 H8 O7 C(C(=O)O)C....
19 3N36 - GLA C6 H12 O6 C([C@@H]1[....
20 1AX0 Ka = 1340 M^-1 A2G C8 H15 N O6 CC(=O)N[C@....
21 1UZY - GAL BGC n/a n/a
22 1LTE - BGC GAL n/a n/a
23 1AX1 Ka = 1940 M^-1 BGC GAL n/a n/a
24 1AX2 Ka = 9730 M^-1 NDG GAL n/a n/a
25 1GZC Kd = 0.32 mM LAT C12 H22 O11 C([C@@H]1[....
26 3N35 - A2G C8 H15 N O6 CC(=O)N[C@....
27 1AXZ Ka = 1570 M^-1 GAL C6 H12 O6 C([C@@H]1[....
28 1GZ9 Kd = 0.31 mM FUC LAT n/a n/a
29 3ZYR Kd = 4.6 uM ASN NAG NAG BMA MAN MAN NAG NAG n/a n/a
30 3ZVX - MAN MAN MAN n/a n/a
31 5KXE Kd = 5.45 uM 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
32 5KXB - NGA C8 H15 N O6 CC(=O)N[C@....
33 5KXC - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
34 5KXD - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
35 4WV8 - LBT C12 H22 O11 C([C@@H]1[....
36 4U2A - A2G C8 H15 N O6 CC(=O)N[C@....
37 4U36 - TNR C11 H20 N2 O8 CC(=O)N[C@....
38 1JXN - MFU C7 H14 O5 C[C@H]1[C@....
39 3WCS - MAN NAG GAL n/a n/a
40 3WOG - MAN NAG n/a n/a
41 5EYX - MDM C13 H24 O11 CO[C@@H]1[....
42 5EYY - MDM C13 H24 O11 CO[C@@H]1[....
43 2BQP - GLC C6 H12 O6 C([C@@H]1[....
44 5T7P - XMM C14 H15 Br Cl N O6 c1cc(c(c2c....
45 2DVA - GAL MGC n/a n/a
46 2DV9 - GAL GAL n/a n/a
47 1V6K - GAL GLC n/a n/a
48 1V6L - GAL BGC n/a n/a
49 2DVD - GAL GAL n/a n/a
50 2TEP - GAL NGA n/a n/a
51 2DVB - GAL C6 H12 O6 C([C@@H]1[....
52 1V6I - GAL GLC n/a n/a
53 2PEL Ki = 1.37 mM LAT C12 H22 O11 C([C@@H]1[....
54 1G9F - GAL NAG GAL NAG GAL n/a n/a
55 2DTW - 2GS C7 H14 O6 CO[C@@H]1[....
56 1WBL - AMG C7 H14 O6 CO[C@@H]1[....
57 2ZMK - GLA EGA n/a n/a
58 2D3S - TNR C11 H20 N2 O8 CC(=O)N[C@....
59 2FMD - MAN MAN n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MDM; Similar ligands found: 199
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL MBG 1 1
2 M13 1 1
3 MDM 1 1
4 MAN MMA MAN 0.696429 1
5 BGC BGC BGC ASO BGC BGC ASO 0.641509 0.942857
6 BGC BGC BGC BGC BGC 0.641509 0.942857
7 BGC BGC BGC GLC BGC BGC 0.641509 0.942857
8 BGC BGC BGC 0.641509 0.942857
9 GLC BGC BGC BGC BGC BGC BGC 0.641509 0.942857
10 GLC BGC BGC BGC 0.641509 0.942857
11 GLA MBG 0.62 1
12 WZ3 0.619048 0.972222
13 MMA MAN 0.615385 1
14 DR5 0.615385 1
15 GYP 0.613636 0.914286
16 MMA 0.613636 0.914286
17 MBG 0.613636 0.914286
18 AMG 0.613636 0.914286
19 LB2 0.607843 0.942857
20 M3M 0.607843 0.942857
21 MAN GLC 0.607843 0.942857
22 GLA GAL GAL 0.596491 0.942857
23 GLA GAL BGC 0.596491 0.942857
24 TRE 0.590909 0.942857
25 NAG MBG 0.583333 0.744681
26 MAN MAN MAN GLC 0.57377 0.942857
27 XLM 0.561404 0.972222
28 GAL MGC 0.559322 0.744681
29 BGC BGC BGC BGC 0.557377 0.942857
30 BGC BGC BGC BGC BGC BGC BGC BGC 0.557377 0.942857
31 NAG BMA MAN MAN MAN MAN MAN 0.549296 0.921053
32 MAN BMA NAG 0.530303 0.73913
33 GLA GAL NAG 0.530303 0.73913
34 NAG GAL GAL 0.530303 0.73913
35 BGC BGC 0.528302 0.942857
36 MAN MAN 0.528302 0.942857
37 LAT GLA 0.528302 0.942857
38 2M4 0.528302 0.942857
39 BGC BGC GLC 0.525424 0.942857
40 NAG MAN MMA 0.507246 0.744681
41 OPM MAN MAN 0.492754 0.809524
42 P3M 0.492308 0.733333
43 BMA MAN MAN 0.491803 0.942857
44 BMA MAN 0.491228 0.864865
45 DOM 0.491228 0.891892
46 BMA BMA 0.490909 0.942857
47 GLC BGC 0.490909 0.942857
48 GLA GLA 0.490909 0.942857
49 LAT 0.490909 0.942857
50 LBT 0.490909 0.942857
51 CBI 0.490909 0.942857
52 BGC GLC 0.490909 0.942857
53 GLA GAL 0.490909 0.942857
54 MAB 0.490909 0.942857
55 BGC BMA 0.490909 0.942857
56 GAL BGC 0.490909 0.942857
57 N9S 0.490909 0.942857
58 BMA GAL 0.490909 0.942857
59 MAL MAL 0.490909 0.916667
60 B2G 0.490909 0.942857
61 BGC GAL 0.490909 0.942857
62 MAL 0.490909 0.942857
63 CBK 0.490909 0.942857
64 GAL GLC 0.490909 0.942857
65 GLC GAL 0.490909 0.942857
66 GLA MMA ABE 0.485294 0.921053
67 MAN MAN BMA MAN 0.484848 0.942857
68 MAN MAN MAN MAN 0.484848 0.942857
69 BMA BMA MAN 0.482759 0.916667
70 GAL FUC 0.482759 0.942857
71 4MU MAN MAN 0.48 0.772727
72 BGC BGC ZZ1 0.48 0.772727
73 M5S 0.477612 0.942857
74 MAN BMA MAN MAN MAN 0.477612 0.942857
75 CGC 0.47541 0.888889
76 GLA EGA 0.474576 0.944444
77 NOY BGC 0.474576 0.717391
78 RZM 0.473684 0.659574
79 FUC GLA GLA 0.46875 0.971429
80 GLA GLA FUC 0.46875 0.971429
81 GAL GAL SO4 0.46875 0.673469
82 GLA GAL FUC 0.46875 0.971429
83 GAL GAL FUC 0.46875 0.971429
84 FUC GAL GLA 0.46875 0.971429
85 MAN MAN BMA 0.466667 0.942857
86 MAN H1M MAN 0.463768 0.921053
87 GTM BGC BGC 0.463768 0.921053
88 GAL NGA 0.460317 0.73913
89 GAL A2G 0.460317 0.73913
90 A2G GAL 0.460317 0.73913
91 LAT NAG GAL 0.459459 0.73913
92 BGC GAL NAG GAL 0.459459 0.73913
93 GAL NAG GAL BGC 0.459459 0.73913
94 NOJ GLC 0.459016 0.695652
95 GLC DMJ 0.459016 0.695652
96 GLC BGC BGC 0.457627 0.942857
97 GLC BGC BGC BGC BGC BGC 0.457627 0.942857
98 MT7 0.457627 0.942857
99 GLC BGC BGC BGC BGC 0.457627 0.942857
100 BGC GLC GLC 0.457627 0.942857
101 CTR 0.457627 0.942857
102 BMA BMA BMA 0.457627 0.942857
103 DXI 0.457627 0.942857
104 MAN BMA BMA BMA BMA 0.457627 0.942857
105 GLC GLC GLC GLC GLC GLC GLC GLC 0.457627 0.942857
106 BGC GLC GLC GLC GLC 0.457627 0.942857
107 MAN MAN BMA BMA BMA BMA 0.457627 0.942857
108 CEY 0.457627 0.942857
109 CTT 0.457627 0.942857
110 GLC GLC GLC GLC GLC 0.457627 0.942857
111 GLC GAL GAL 0.457627 0.942857
112 MLR 0.457627 0.942857
113 U63 0.457627 0.846154
114 BMA BMA BMA BMA BMA BMA 0.457627 0.942857
115 MAN BMA BMA 0.457627 0.942857
116 BMA MAN BMA 0.457627 0.942857
117 GLA GAL GLC 0.457627 0.942857
118 BGC GLC GLC GLC GLC GLC GLC 0.457627 0.942857
119 CE8 0.457627 0.942857
120 CT3 0.457627 0.942857
121 BGC GLC GLC GLC 0.457627 0.942857
122 BGC BGC BGC GLC 0.457627 0.942857
123 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.457627 0.942857
124 CE5 0.457627 0.942857
125 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.457627 0.942857
126 MTT 0.457627 0.942857
127 GLC GLC GLC GLC GLC GLC GLC 0.457627 0.942857
128 B4G 0.457627 0.942857
129 CEX 0.457627 0.942857
130 BMA BMA BMA BMA BMA 0.457627 0.942857
131 GLC GLC BGC 0.457627 0.942857
132 GLC GLC BGC GLC GLC GLC GLC 0.457627 0.942857
133 GLC BGC GLC 0.457627 0.942857
134 BGC BGC BGC BGC BGC BGC 0.457627 0.942857
135 CE6 0.457627 0.942857
136 GAL GAL GAL 0.457627 0.942857
137 NAG GAL GAL NAG 0.453333 0.693878
138 NAG GAL GAL NAG GAL 0.453333 0.693878
139 GAL NAG GAL NAG GAL NAG 0.453333 0.68
140 5QP 0.45 0.837838
141 FRU GAL 0.45 0.8
142 BMA FRU 0.45 0.8
143 T6P 0.448276 0.733333
144 MAN MMA 0.448276 1
145 GLC GAL NAG GAL 0.447368 0.73913
146 BGC OXZ 0.442623 0.64
147 IFM BMA 0.442623 0.711111
148 MAN MNM 0.442623 0.717391
149 9MR 0.442623 0.711111
150 BMA IFM 0.442623 0.711111
151 MAL EDO 0.442623 0.891892
152 IFM BGC 0.442623 0.711111
153 MAN 7D1 0.440678 0.842105
154 GLC GLC GLC GLC 0.439394 0.942857
155 MGL SGC GLC GLC 0.438356 0.921053
156 BGC BGC SGC MGL 0.438356 0.921053
157 MAN MAN MAN BMA MAN 0.438356 0.942857
158 GLA GAL BGC 5VQ 0.4375 0.894737
159 NLC 0.4375 0.73913
160 8VZ 0.4375 0.68
161 NDG GAL 0.4375 0.73913
162 GAL NDG 0.4375 0.73913
163 GAL NGA GLA BGC GAL 0.435897 0.73913
164 FMO 0.435484 0.825
165 MAG FUC GAL 0.430556 0.729167
166 ABL 0.428571 0.673469
167 MAN BMA BMA BMA BMA BMA 0.428571 0.916667
168 MVP 0.428571 0.702128
169 BMA BMA BMA BMA BMA BMA MAN 0.428571 0.916667
170 NAG NAG BMA MAN 0.426829 0.641509
171 NOK GAL 0.426471 0.6
172 NGT GAL 0.426471 0.666667
173 GAL NGT 0.426471 0.666667
174 GAL NOK 0.426471 0.6
175 MAN DGO 0.42623 0.864865
176 GLA MAN ABE 0.422535 0.918919
177 MAN MAN MAN BMA MAN MAN MAN 0.419753 1
178 FUC BGC GAL 0.41791 0.971429
179 GLA GAL GLC NBU 0.41791 0.85
180 NAG BMA 0.41791 0.66
181 4RS 0.415385 0.829268
182 GAL NGA A2G 0.414286 0.68
183 NAG GAL BGC 0.413333 0.73913
184 NGA SER GAL 0.410959 0.68
185 GAL TNR 0.410959 0.68
186 GAL SER A2G 0.410959 0.68
187 A2G SER GAL 0.410959 0.68
188 WZ5 0.406977 0.744681
189 GLC 7LQ 0.40625 0.837838
190 LMU 0.405797 0.790698
191 LMT 0.405797 0.790698
192 UMQ 0.405797 0.790698
193 DMU 0.405797 0.790698
194 GLC GLC XYP 0.405797 0.942857
195 NGA GLA GAL BGC 0.405063 0.73913
196 BTU 0.403226 0.8
197 TUR 0.403226 0.8
198 BGC GLA GAL FUC 0.4 0.971429
199 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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5eyy.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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