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Receptor
PDB id Resolution Class Description Source Keywords
4YEF 1.72 Å EC: 2.-.-.- BETA1 CARBOHYDRATE BINDING MODULE (CBM) OF AMP-ACTIVATED PRO KINASE (AMPK) IN COMPLEX WITH GLUCOSYL-BETA-CYCLODODEXTRIN RATTUS NORVEGICUS CARBOHYDRATE BINDING MODULE CBM AMPK AMP-ACTIVATED PROTEICYCLODEXTRIN SUGAR BINDING PROTEIN
Ref.: DETERMINANTS OF OLIGOSACCHARIDE SPECIFICITY OF THE CARBOHYDRATE-BINDING MODULES OF AMP-ACTIVATED PROTE KINASE. BIOCHEM.J. V. 468 245 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4CQ G:202;
B:201;
E:201;
A:201;
D:201;
C:201;
F:201;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
Kd = 4.44 uM
1297.12 C48 H80 O40 C([C@...
SO4 F:202;
B:202;
B:203;
D:202;
E:203;
E:202;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
GOL A:202;
C:202;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YEF 1.72 Å EC: 2.-.-.- BETA1 CARBOHYDRATE BINDING MODULE (CBM) OF AMP-ACTIVATED PRO KINASE (AMPK) IN COMPLEX WITH GLUCOSYL-BETA-CYCLODODEXTRIN RATTUS NORVEGICUS CARBOHYDRATE BINDING MODULE CBM AMPK AMP-ACTIVATED PROTEICYCLODEXTRIN SUGAR BINDING PROTEIN
Ref.: DETERMINANTS OF OLIGOSACCHARIDE SPECIFICITY OF THE CARBOHYDRATE-BINDING MODULES OF AMP-ACTIVATED PROTE KINASE. BIOCHEM.J. V. 468 245 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 269 families.
1 4YEF Kd = 4.44 uM 4CQ C48 H80 O40 C([C@@H]1[....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 237 families.
1 1Z0M - BCD C42 H70 O35 C([C@@H]1[....
2 1Z0N - BCD C42 H70 O35 C([C@@H]1[....
3 4YEE Kd = 0.32 uM 4CQ C48 H80 O40 C([C@@H]1[....
4 4YEF Kd = 4.44 uM 4CQ C48 H80 O40 C([C@@H]1[....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 1Z0M - BCD C42 H70 O35 C([C@@H]1[....
2 1Z0N - BCD C42 H70 O35 C([C@@H]1[....
3 4YEE Kd = 0.32 uM 4CQ C48 H80 O40 C([C@@H]1[....
4 4YEF Kd = 4.44 uM 4CQ C48 H80 O40 C([C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4CQ; Similar ligands found: 37
No: Ligand ECFP6 Tc MDL keys Tc
1 4CQ 1 1
2 BCD 0.529412 0.911765
3 ACX 0.529412 0.911765
4 GLC GLC GLC GLC GLC GLC GLC GLC 0.529412 0.911765
5 GLC GLC GLC GLC GLC GLC GLC 0.529412 0.911765
6 GLC GLC GLC GLC GLC GLC 0.529412 0.911765
7 RCD 0.529412 0.911765
8 MAN MMA 0.5 0.916667
9 BGC GLC 0.483871 0.970588
10 GLA GLC 0.483871 0.970588
11 BMA GLA 0.483871 0.970588
12 GLA BMA 0.483871 0.970588
13 BMA MAN 0.483871 0.970588
14 BGC GLA 0.483871 0.970588
15 GLC BGC 0.483871 0.970588
16 GLA BGC 0.483871 0.970588
17 GLC GLC 0.483871 0.970588
18 MAN MAN 0.483871 0.970588
19 LAK 0.483871 0.970588
20 GAL GAL 0.483871 0.970588
21 MLB 0.483871 0.970588
22 GAL GLC 0.483871 0.970588
23 MAN BMA 0.483871 0.970588
24 GLC GLC GLC GLC GLC BGC 0.46875 0.970588
25 MAN MAN MAN 0.46875 0.970588
26 GLC GLC GLC 0.46875 0.970588
27 BMA MAN MAN 0.46875 0.970588
28 GLC GLC GLC GLC BGC 0.46875 0.970588
29 AHR AHR 0.42623 0.833333
30 FUB AHR 0.42623 0.833333
31 MAN BMA MAN 0.416667 0.970588
32 WZ2 0.415584 0.846154
33 AHR AHR AHR AHR AHR AHR 0.40625 0.833333
34 FUB AHR AHR 0.40625 0.833333
35 MAN MMA MAN 0.405405 0.916667
36 DMJ MAN 0.4 0.680851
37 NOJ BGC 0.4 0.680851
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found with APoc: 66
This union binding pocket(no: 1) in the query (biounit: 4yef.bio5) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 1LR8 IHS None
2 3SJU NDP None
3 3MEH THP None
4 4O1M NAD None
5 4J4H NAI None
6 4J4H 1J1 None
7 3F5O UOC COA None
8 1WAP TRP None
9 3NUG NAD None
10 5AGR A52 None
11 4JGP PYR None
12 4IPH 1FJ None
13 3CTL S6P None
14 2CNT COA 2.24719
15 1CX9 NHP 3.37079
16 4M1U MBG A2G 5.61798
17 4M1U A2G MBG 5.61798
18 1ZMT RNO 5.61798
19 6MB9 NMY 5.61798
20 5A7Y SAH 5.61798
21 4POS NAG SIA GAL 5.61798
22 4X17 SIA SIA 6.74157
23 2AG5 NAD 6.74157
24 4X17 SIA 6.74157
25 1U1B PAX 6.74157
26 5WQP NAP 6.74157
27 5WQP NCA 6.74157
28 3LPP KTL 6.74157
29 5C8W PCG 6.74157
30 4R84 CSF 7.86517
31 2X52 GYT 7.86517
32 2OFV 242 7.86517
33 4HK8 XYP XYP XYP XYP XYP XYP 7.86517
34 4GN8 ASO 7.86517
35 3MBI ADP 7.86517
36 1WN3 HXC 8.98876
37 4I9B NAD 8.98876
38 5G5G FAD 8.98876
39 5ESO ISC 8.98876
40 5ESO TDP 8.98876
41 1SL4 MAN MAN MAN MAN 8.98876
42 5A89 FMN 8.98876
43 4AMW 5DI 10.1124
44 5AVF TAU 10.1124
45 5KL0 G16 11.236
46 5MU6 KFK 11.236
47 5MU6 MYA 11.236
48 1VC9 ATP 11.236
49 4MBY BGC SIA GAL 11.236
50 4CFP NAG AMU NAG AMV 12.3596
51 5GQF GAL NAG 12.3596
52 2QO4 CHD 13.4831
53 5HJO XD3 13.4831
54 5GWE GWM 13.4831
55 3VHH VHH 14.6067
56 3GX0 GDS 14.6067
57 5WA0 MSS 15.7303
58 2X9L BOG 17.9775
59 5O2N NAG NAG NDG NAG 17.9775
60 5O2N NAG 17.9775
61 4HJY NAG NAG NAG 21.3483
62 1N0U SO1 22.4719
63 4GIM PSU 24.7191
64 3HNT AXR BXY BXY BXX 30.3371
65 1QHO MAL 43.8202
66 4PYH GLC GLC GLC GLC GLC GLC 48.3146
Pocket No.: 2; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found with APoc: 7
This union binding pocket(no: 2) in the query (biounit: 4yef.bio2) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 4WB7 ATP None
2 6MB9 COA 5.61798
3 3PFD FDA 5.61798
4 4NTM 2K8 8.98876
5 2BIW 3ON 12.3596
6 1PK8 ATP 12.3596
7 3KLL MAL 17.9775
Pocket No.: 3; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found with APoc: 178
This union binding pocket(no: 3) in the query (biounit: 4yef.bio4) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 4K49 HFQ None
2 1E7S NAP None
3 3TAY MN0 None
4 4MZQ 1VU None
5 4F07 FAD None
6 4MN3 ACE PHE ALA TYR M3L SER NH2 None
7 5EPL 5R0 PHE ALA LEU ELY 5R5 None
8 6GEH FAD None
9 2X3F APC None
10 2WEI VGG None
11 2DT5 NAD None
12 1R4W GSH None
13 2HFP NSI None
14 2WYV NAD None
15 1UGX GAL MGC None
16 6E2B PT7 None
17 1NNU TCT None
18 1NNU NAD None
19 2PRG BRL None
20 2NPA MMB None
21 2CYE COA None
22 6CI9 NAP None
23 5KK4 44E None
24 3BJK CIT None
25 3FPF TNA 1.1236
26 3FPF MTA 1.1236
27 5Z49 RUB 2.24719
28 3W6C NAG NAG 3.37079
29 2FZW NAD 3.37079
30 1NXJ TLA 3.37079
31 3P48 DUP 3.37079
32 1L1E SAH 3.37079
33 3R35 4CO 4.49438
34 6EL3 NAP 4.49438
35 4E5N NAD 4.49438
36 5DEY 59T 4.49438
37 4R0M FA5 4.49438
38 2FK8 SAM 4.49438
39 1QG6 TCL 4.49438
40 3GE7 AFQ 4.49438
41 3UXL CFI 4.49438
42 1WPY BTN 4.49438
43 2PZM NAD 5.61798
44 2PZM UDP 5.61798
45 5N9T 8QQ 5.61798
46 4QAC KK3 5.61798
47 6C1S EFV 5.61798
48 1I36 NAP 5.61798
49 3KO8 NAD 5.61798
50 1M0W 3GC 5.61798
51 2G50 PYR 5.61798
52 1WPQ NAD 5.61798
53 4I42 1HA 5.61798
54 3DLG GWE 5.61798
55 4K38 SAM 5.61798
56 6ASZ GLN THR ALA ARG M3L SER 6.74157
57 5AE9 OKO 6.74157
58 4ZTE 4RL 6.74157
59 3EM0 CHD 6.74157
60 4UUW AMP 6.74157
61 3ZV6 4HB 6.74157
62 3ZV6 NAD 6.74157
63 4I3V NAD 6.74157
64 3L9R L9R 6.74157
65 4P5Z Q7M 6.74157
66 5VC5 96M 6.74157
67 2JFN UMA 6.74157
68 1JJE BYS 6.74157
69 2Q1W NAD 6.74157
70 1SL3 170 6.74157
71 4PAB THG 6.74157
72 4ZFL 4NK 6.74157
73 2RCU BUJ 6.74157
74 1ULM NAG NAG NAG 7.31707
75 5N0J FAD 7.86517
76 2D37 FMN 7.86517
77 2D37 NAD 7.86517
78 4FBL SPD 7.86517
79 3OV6 MK0 7.86517
80 1WOR RED 7.86517
81 3IGO ANP 7.86517
82 1H74 ADP 7.86517
83 3AB4 LYS 7.86517
84 3AB4 THR 7.86517
85 5L9G MO0 7.86517
86 3JWH SAH 7.86517
87 4GA6 AMP 7.86517
88 1VL8 NAP 7.86517
89 1EQ2 NAP 8.98876
90 5KBZ 3B2 8.98876
91 3MKK GLC BGC 8.98876
92 4XJ2 FMN 8.98876
93 5XKT GNP 8.98876
94 2X6T NAP 8.98876
95 5A89 ADP 8.98876
96 2G30 ALA ALA PHE 8.98876
97 2ZUX RAM 8.98876
98 2ZAT NAP 8.98876
99 2GC0 PAN 10.1124
100 1GZ6 NAI 10.1124
101 4J1Q NDP 10.1124
102 5UAV NDP 10.1124
103 1VEM GLC GLC 10.1124
104 5UAV TFB 10.1124
105 5DF1 58X 10.1124
106 5DF1 NAP 10.1124
107 5WP5 SAH 10.1124
108 4I4Z 2NE 10.1124
109 3G5D 1N1 10.1124
110 5BJX NAD 10.1124
111 2ART LPA AMP 10.1124
112 4COL DTP 10.1124
113 3OJF IMJ 10.1124
114 3X44 PUS 10.1124
115 3OJF NDP 10.1124
116 1U7T TDT 11.236
117 4ZRN NAD 11.236
118 1U7T NAD 11.236
119 4ZRN UPG 11.236
120 1QPR PPC 11.236
121 1ZVW PRP 11.236
122 1HYH NAD 11.236
123 5GT9 NAP 11.236
124 5Z21 NAI 11.236
125 3HUJ AGH 11.236
126 1RZ0 FAD 11.236
127 4K4D HFQ 12.3596
128 2FR1 NDP 12.3596
129 1GT4 UNA 12.3596
130 1Z6Z NAP 12.3596
131 4A22 TD4 12.3596
132 5MSO NAP 12.3596
133 2OO8 RAJ 12.3596
134 3UKR CKH 13.4831
135 6DNT NAD 13.4831
136 4KBA 1QM 13.4831
137 4ONA UW1 13.4831
138 3AD8 FAD 13.4831
139 3AD8 PYC 13.4831
140 5H9O GLC 13.4831
141 4JAW NGT GAL 13.4831
142 5J32 IPM 13.4831
143 1MI3 NAD 13.4831
144 1JQN DCO 14.6067
145 3F10 8HG 14.6067
146 6G09 BXP 14.6067
147 2PD4 DCN 14.6067
148 1EN2 NAG NAG NAG NAG 14.6067
149 1EHH NAG NAG NAG 14.6067
150 5ACM MBT 15.7303
151 5Z54 0HZ 15.7303
152 3ZXR IQ1 15.7303
153 3ZXR P3S 15.7303
154 1BDB NAD 15.7303
155 2X24 X24 15.7303
156 1GEE NAD 15.7303
157 2Z49 AMG 16.8539
158 4CQE CQE 16.8539
159 5LYR MAN MNM 17.9775
160 4ZAH T5K 17.9775
161 5J75 6GQ 19.1011
162 3CH6 NAP 19.1011
163 3CH6 311 19.1011
164 3WXB NDP 19.1011
165 6GWR FEW 20.2247
166 1E3W NAD 20.2247
167 1JG3 VAL TYR PRO IAS HIS ALA 20.2247
168 2ED4 FAD 21.3483
169 5UE4 5XQ 21.3483
170 3AHO 3A2 22.4719
171 1XKQ NDP 22.4719
172 2GAG FOA 23.5955
173 2GAG FAD 23.5955
174 2BLN U5P 24.7191
175 1GVF PGH 26.9663
176 1Z45 NAD 30.3371
177 1MEX RAC 30.3371
178 4Z9D NAD 31.4607
Pocket No.: 4; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4yef.bio7) has 32 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found with APoc: 20
This union binding pocket(no: 5) in the query (biounit: 4yef.bio6) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 6EMU SAM None
2 4R78 AMP None
3 4NVQ 2OD None
4 4NVQ SAH None
5 1PZG A3D 3.37079
6 2BRY FAD 4.49438
7 4XVX P33 FDA 5.61798
8 3G08 FEE 6.74157
9 1XG5 NAP 6.74157
10 4CTA ATP 6.74157
11 2CHT TSA 7.86517
12 1ORR NAD 7.86517
13 5DQ8 FLF 7.86517
14 2C29 NAP 7.86517
15 1GQG DCD 13.4831
16 5W4W 9WG 13.4831
17 3T6E MQ9 13.4831
18 3RFV NAI 14.6067
19 4PW9 MSS 15.7303
20 5Y1G AKB 22.4719
Pocket No.: 6; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found with APoc: 46
This union binding pocket(no: 6) in the query (biounit: 4yef.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 5YSS NAD None
2 6CI9 F3V None
3 3DWQ NGC GAL NGA POL AZI None
4 2BD0 NAP None
5 2Z9C FMN None
6 2Z9C DTC None
7 3QWI NAP None
8 1I82 BGC BGC 2.24719
9 6DND PLP 2.24719
10 2P1C GG3 2.24719
11 5O42 NAD 2.24719
12 5O42 9JW 2.24719
13 5O42 BGC 2.24719
14 2C5A NAD 3.37079
15 2C5A GDC 3.37079
16 1WK9 TSB 3.37079
17 2V0C ANZ 4.49438
18 1QG6 NAD 4.49438
19 2CFC NAD 5.61798
20 1NJJ ORX 5.61798
21 5GWT NAD 5.61798
22 5Z2L NDP 5.61798
23 6F6D AKG 6.74157
24 5V3Y 5V8 6.74157
25 4GV8 DUP 6.74157
26 1CX4 CMP 6.74157
27 2AE2 PTO 7.86517
28 2AE2 NAP 7.86517
29 1G8K MGD 7.86517
30 4RKC PMP 7.86517
31 5ZA2 NXL 7.86517
32 4JEJ 1GP 8.98876
33 3PDB PMP 8.98876
34 2DTX BMA 10.1124
35 1RX0 FAD 10.1124
36 4C0X FMN 10.1124
37 4C0X AQN 10.1124
38 1UWC FER 11.236
39 4HVA 4HV 11.236
40 1UXX XYP XYP XYP XYP XYP 12.3596
41 1N62 FAD 13.4831
42 2PD4 NAD 14.6067
43 3DWB RDF 14.6067
44 1IYK MIM 16.8539
45 1NFQ NAI 17.9775
46 3AVR OGA 23.5955
Pocket No.: 7; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found with APoc: 1
This union binding pocket(no: 7) in the query (biounit: 4yef.bio3) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 4AT3 LTI 5.61798
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