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Receptor
PDB id Resolution Class Description Source Keywords
5XG5 1.54 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF MITSUBA-1 WITH BOUND NACGAL SYNTHETIC CONSTRUCT PROTEIN DESIGN LECTIN DE NOVO PROTEIN SUGAR BINDING PROTE
Ref.: COMPUTATIONAL DESIGN OF A SYMMETRICAL BETA-TREFOIL WITH CANCER CELL BINDING ACTIVITY. SCI REP V. 7 5943 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
A2G A:201;
A:203;
A:202;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 0.33 mM
221.208 C8 H15 N O6 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5XG5 1.54 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF MITSUBA-1 WITH BOUND NACGAL SYNTHETIC CONSTRUCT PROTEIN DESIGN LECTIN DE NOVO PROTEIN SUGAR BINDING PROTE
Ref.: COMPUTATIONAL DESIGN OF A SYMMETRICAL BETA-TREFOIL WITH CANCER CELL BINDING ACTIVITY. SCI REP V. 7 5943 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5XG5 Kd = 0.33 mM A2G C8 H15 N O6 CC(=O)N[C@....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 5XG5 Kd = 0.33 mM A2G C8 H15 N O6 CC(=O)N[C@....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 298 families.
1 5XG5 Kd = 0.33 mM A2G C8 H15 N O6 CC(=O)N[C@....
2 5F90 Kd = 14 uM GLA GAL BGC 5VQ n/a n/a
3 5F8Y Kd = 57 uM X6X C6 H13 N O5 C([C@@H]1[....
4 5F8W Kd = 51 uM GLA C6 H12 O6 C([C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A2G; Similar ligands found: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 NGA 1 1
2 NAG 1 1
3 A2G 1 1
4 BM3 1 1
5 HSQ 1 1
6 NDG 1 1
7 BGN 0.638298 0.888889
8 SIZ 0.630435 0.906977
9 YX1 0.625 0.65
10 STZ 0.612245 0.65
11 4QY 0.591837 0.735849
12 BMX 0.591837 0.735849
13 16G 0.591837 0.735849
14 9C1 0.58 0.886364
15 SNG 0.5625 0.866667
16 NGS 0.54902 0.661017
17 NDG NAG 0.54386 0.833333
18 CBS 0.54386 0.833333
19 NAG GDL 0.54386 0.833333
20 CBS CBS 0.54386 0.833333
21 ASG 0.538462 0.661017
22 BG8 0.537037 0.906977
23 MAG 0.530612 0.909091
24 2F8 0.530612 0.909091
25 NDG GAL 0.517857 0.888889
26 NLC 0.517857 0.888889
27 GAL NDG 0.517857 0.888889
28 NAG A2G 0.517241 0.833333
29 4V5 0.517241 0.829787
30 NAG NGA 0.517241 0.833333
31 4UZ 0.508475 0.808511
32 NAG NAG NAG NAG NDG 0.508197 0.816327
33 NDG NAG NAG NAG 0.508197 0.816327
34 NAG NAG NDG 0.508197 0.816327
35 NAG NAG NDG NAG 0.508197 0.816327
36 CTO 0.508197 0.816327
37 NDG NAG NAG NDG 0.508197 0.816327
38 NAG NAG NAG NDG 0.508197 0.816327
39 NDG NAG NAG 0.508197 0.816327
40 NAG NAG NAG NAG NAG 0.508197 0.816327
41 NAG NAG NAG NAG NAG NAG 0.508197 0.816327
42 NAG NAG NAG NAG NAG NAG NAG NAG 0.508197 0.816327
43 MQG 0.5 0.698113
44 NBG 0.5 0.951219
45 GAL NGA 0.491228 0.888889
46 A2G GAL 0.491228 0.888889
47 GAL A2G 0.491228 0.888889
48 AMU 0.490909 0.930233
49 NG1 0.490566 0.754717
50 GN1 0.490566 0.754717
51 NAG GAL 0.474576 0.888889
52 GAL NAG 0.474576 0.888889
53 NAG FUC 0.474576 0.866667
54 NAG GAL NAG 0.455882 0.833333
55 3YW 0.448276 0.930233
56 GLA GAL NAG 0.446154 0.888889
57 MAN BMA NAG 0.446154 0.888889
58 NGA GAL 0.428571 0.869565
59 FUC GAL NAG 0.426471 0.869565
60 GAL NAG FUC 0.426471 0.869565
61 DR2 0.426471 0.869565
62 NAG GAL FUC 0.426471 0.869565
63 NDG GAL FUC 0.426471 0.869565
64 FUC GAL NDG 0.426471 0.869565
65 FUL GAL NAG 0.426471 0.869565
66 G6S NAG 0.426471 0.645161
67 TNR 0.42623 0.833333
68 GYU 0.42623 0.740741
69 GAL NGA A2G 0.424242 0.833333
70 NAG BDP 0.421875 0.851064
71 NAG MBG 0.419355 0.851064
72 NGA GAL BGC 0.41791 0.888889
73 NAG NDG 0.415385 0.784314
74 NAG NAG 0.415385 0.784314
75 AZC 0.415094 0.795918
76 SN5 SN5 0.412698 0.705882
77 A2G MBG 0.412698 0.851064
78 MBG A2G 0.412698 0.851064
79 HS2 0.411765 0.8125
80 5AX 0.411765 0.866667
81 NAG MAN BMA 0.411765 0.888889
82 6ZC 0.409091 0.655738
83 LEC 0.409091 0.655738
84 TCG 0.408451 0.689655
85 GAL BGC NAG GAL 0.408451 0.888889
86 NAG MAN 0.40625 0.851064
87 WOO 0.404762 0.7
88 MAN 0.404762 0.7
89 GAL 0.404762 0.7
90 BGC 0.404762 0.7
91 BMA 0.404762 0.7
92 GLA 0.404762 0.7
93 ALL 0.404762 0.7
94 GLC 0.404762 0.7
95 GXL 0.404762 0.7
96 GIV 0.404762 0.7
97 NAG AMU 0.402778 0.8
98 NAG MUB 0.402778 0.8
99 NAG A2G GAL 0.402778 0.833333
100 A2G GAL FUC 0.4 0.869565
101 FUC GLA A2G 0.4 0.869565
102 DR3 0.4 0.869565
103 A2G GLA FUC 0.4 0.869565
104 NGA GAL FUC 0.4 0.869565
105 FUC GAL A2G 0.4 0.869565
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5XG5; Ligand: A2G; Similar sites found with APoc: 112
This union binding pocket(no: 1) in the query (biounit: 5xg5.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 3BL7 DD1 None
2 1ST0 GTG None
3 2ZQO NGA None
4 5WA9 9ZD None
5 2GQR ADP None
6 2GQS ADP None
7 1OG1 TAD None
8 5RHN 8BR None
9 1DQX BMP None
10 2Z49 AMG None
11 4I42 1HA None
12 2WCV FUC None
13 2Z48 NGA None
14 2Z48 A2G None
15 5ZAI COA None
16 5C9P FUC None
17 2VSS ACO None
18 5H4S RAM None
19 1GHE ACO None
20 1VDC FAD 1.37931
21 1CR1 TTP 1.37931
22 3TW1 AHN 1.37931
23 4R57 ACO 1.37931
24 1LLF F23 1.37931
25 2VSU ACO 1.37931
26 4N9I PCG 2.06897
27 3KMW ATP 2.06897
28 1LOB MMA 2.06897
29 5N1P 8GK 2.06897
30 2C0U FAD NBT 2.06897
31 5NC9 8SZ 2.06897
32 3A6T 8OG 2.32558
33 4HKP TKW 2.75862
34 4UP3 FAD 2.75862
35 1B1C FMN 2.75862
36 2FY3 CHT 2.75862
37 3AKK ADP 2.75862
38 4M26 ZZU 2.75862
39 4M26 SIN 2.75862
40 2QCD U5P 2.75862
41 3GLC R5P 2.75862
42 4Q5H ANP 2.75862
43 5HZ9 5M8 2.96296
44 4WOP CTP 3.11111
45 5XFI NAG NAG BMA MAN MAN NAG GAL NAG 3.44828
46 2Q4H AMP 3.44828
47 5LB3 ADP 3.44828
48 1C1X HFA 3.44828
49 2E7Z MGD 3.44828
50 1BW9 PPY 3.44828
51 2Q2Y ADP 3.44828
52 2Q2Y MKR 3.44828
53 4FJU NAI 3.44828
54 5GUD NDP 3.44828
55 5GUD 2IT 3.44828
56 1C1D PHE 3.44828
57 1CKM GTP 3.44828
58 2FUE M1P 3.44828
59 1UYY BGC BGC 3.81679
60 1W1A NDG 4.13793
61 1ATL 0QI 4.13793
62 4JWF SAH 4.13793
63 6AIC AMP 4.13793
64 1X9I G6Q 4.13793
65 4FE2 ADP 4.13793
66 4I4Z 2NE 4.13793
67 3UBM COA 4.13793
68 3ITJ FAD 4.82759
69 3A1I UNU 4.82759
70 1NVM NAD 4.82759
71 1TV5 FMN 4.82759
72 2PWY SAH 5.51724
73 3PVW QRX 5.51724
74 4ZGR NGA GAL 6.2069
75 2GU8 796 6.2069
76 6FKW PQQ 6.2069
77 4YNM SAM 6.2069
78 3O7W SAM 6.2069
79 3WO0 ADP 6.89655
80 3WO0 ALA 6.89655
81 1V97 MTE 7.58621
82 4QIJ 1HA 7.58621
83 4M69 ANP 7.58621
84 2VQD AP2 7.58621
85 3VPB ADP 7.58621
86 1TLL FMN 8.27586
87 3PN1 IVH 8.27586
88 5XWC 8GL 8.27586
89 5XWC 2IT 8.27586
90 5XWC NAP 8.27586
91 5JBX COA 8.27586
92 2Z5F A3P 8.27586
93 5O96 SAM 8.96552
94 3NC9 TR3 8.96552
95 2D24 XYS XYS 9.65517
96 2QTR NXX 9.65517
97 3MKH FAD 9.65517
98 5CPS GLC GLC GLC GLC GLC GLC GLC GLC 9.65517
99 5CPS GLC GLC GLC GLC GLC GLC GLC GLC GLC 9.65517
100 2ZWA SAH 10.3448
101 5MUA GAL 11.0345
102 1T8U UAP SGN IDS SGN 11.0345
103 1T8U A3P 11.0345
104 3NBC LAT 11.7241
105 3TKY SAH 11.7241
106 1ZRH A3P 13.1034
107 1VKJ A3P 13.1034
108 4PZ6 GMP 13.1034
109 5ODQ 9SB 14.4828
110 3A23 GAL 15.1724
111 1KNM LAT 15.3846
112 4H2D FMN 28.2759
Pocket No.: 2; Query (leader) PDB : 5XG5; Ligand: A2G; Similar sites found with APoc: 33
This union binding pocket(no: 2) in the query (biounit: 5xg5.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 6BSX E7S None
2 1XP8 AGS None
3 5BQ5 ADP BEF None
4 5MEX PAP None
5 1TMM HHR 2.06897
6 1TMM APC 2.06897
7 1OYY AGS 2.75862
8 4HKP 16B 2.75862
9 2AR6 NAG MAN MAN MAN NAG 2.75862
10 1W5F G2P 3.39943
11 1YQD NAP 3.44828
12 1WUU ANP 3.44828
13 3P3G UKW 4.13793
14 3P3G 3P3 4.13793
15 2ZFI ADP 4.13793
16 1EZ0 NAP 4.13793
17 4LPS GDP 4.13793
18 5E1M SAH 4.82759
19 1RE8 BD2 6.2069
20 3KOX Z98 6.2069
21 1QFT HSM 6.2069
22 3TBK ANP 6.89655
23 1MR3 G3D 6.89655
24 5BVE 4VG 7.58621
25 4WNK 453 8.27586
26 5BUK FAD 8.27586
27 4Y0X ADP 8.27586
28 4RD0 GDP 10.3448
29 6DUB SAH 11.0345
30 2CNE DFJ 12.4138
31 4XTX 590 24.8276
32 2IV2 2MD 29.6552
33 5MW8 ATP 32.4138
Pocket No.: 3; Query (leader) PDB : 5XG5; Ligand: A2G; Similar sites found with APoc: 35
This union binding pocket(no: 3) in the query (biounit: 5xg5.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 1HXD BTN None
2 4YC0 5OF None
3 1OJZ NAD None
4 6A4R ASP None
5 1XCL SAH None
6 1NZY BCA 2.06897
7 2V2V V12 2.75862
8 5O1I 9GH 2.75862
9 2FJK 13P 2.75862
10 1RHC F42 ACN 3.44828
11 2OL1 UMP 3.44828
12 3KIF GDL 3.77358
13 2GJ8 ALF GDP 4.13793
14 6C5B SAH 4.13793
15 4GN8 ASO 4.13793
16 3TY5 ATP 4.13793
17 2GSD NAD 4.13793
18 5NUL FMN 5.07246
19 1OBD ATP 5.51724
20 3MB5 SAM 5.51724
21 2NV2 GLN 5.51724
22 2O2C G6Q 6.2069
23 4JIQ 1L5 7.58621
24 4JIQ FMN 7.58621
25 1L3I SAH 8.27586
26 3BER AMP 8.96552
27 5WYF ILP 8.96552
28 2AQJ TRP 10.3448
29 2AQJ FAD 10.3448
30 3MGB PAP 11.7241
31 2CDN ADP 12.4138
32 3BFX A3P 14.4828
33 1JQ3 AAT 16.5517
34 5GUE GGS 22.069
35 2AK3 AMP 30.3448
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