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 MORE than expected: % Diff = 1.75;
Atoms found LESS than expected: % Diff = 0.125;
Atoms found LESS than expected: % Diff = 0.125;
Atoms found LESS than expected: % Diff = 0.125;
Atoms found LESS than expected: % Diff = 0.125;
Atoms found LESS than expected: % Diff = 0.125;
Atoms found LESS than expected: % Diff = 0.125;
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 236 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 211 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 166 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: 25
No: Ligand ECFP6 Tc MDL keys Tc
1 4CQ 1 1
2 BCD 0.529412 0.911765
3 ACX 0.529412 0.911765
4 RCD 0.529412 0.911765
5 MAN MMA 0.5 0.916667
6 BGC GLA 0.483871 0.970588
7 GLA BMA 0.483871 0.970588
8 MAN BMA 0.483871 0.970588
9 BMA GLA 0.483871 0.970588
10 GLA BGC 0.483871 0.970588
11 GAL GAL 0.483871 0.970588
12 LAK 0.483871 0.970588
13 GLA GLC 0.483871 0.970588
14 MLB 0.483871 0.970588
15 GLC GLC GLC GLC BGC 0.46875 0.970588
16 GLC GLC GLC GLC GLC BGC 0.46875 0.970588
17 GLC GLC GLC 0.46875 0.970588
18 MAN MAN MAN 0.46875 0.970588
19 AHR AHR 0.42623 0.833333
20 FUB AHR 0.42623 0.833333
21 WZ2 0.415584 0.846154
22 FUB AHR AHR 0.40625 0.833333
23 AHR AHR AHR 0.40625 0.833333
24 MAN MMA MAN 0.405405 0.916667
25 GLC GLC GLC GLC 0.405405 0.970588
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found: 15
This union binding pocket(no: 1) in the query (biounit: 4yef.bio5) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1LR8 IHS 0.0000952 0.50077 None
2 4O1M NAD 0.01638 0.42916 None
3 4J4H 1J1 0.04244 0.41854 None
4 4J4H NAI 0.04244 0.41854 None
5 4M1U MBG A2G 0.001274 0.48569 5.61798
6 4M1U A2G MBG 0.0003135 0.48172 5.61798
7 2AG5 NAD 0.02209 0.41915 6.74157
8 3LPP KTL 0.008706 0.40439 6.74157
9 5C8W PCG 0.009494 0.4037 6.74157
10 1VC9 ATP 0.01438 0.40882 11.236
11 4CFP NAG AMU NAG AMV 0.02797 0.41486 12.3596
12 5HJO XD3 0.006076 0.40607 13.4831
13 1DWK OXL 0.009907 0.42082 14.6067
14 1N0U SO1 0.01343 0.43952 22.4719
15 3AVS OGA 0.01405 0.40022 23.5955
Pocket No.: 2; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found: 2
This union binding pocket(no: 2) in the query (biounit: 4yef.bio2) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4AMW 5DI 0.0004918 0.40011 10.1124
2 2BIW 3ON 0.02825 0.4015 12.3596
Pocket No.: 3; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found: 30
This union binding pocket(no: 3) in the query (biounit: 4yef.bio4) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4MZQ 1VU 0.0146 0.42971 None
2 4MN3 ACE PHE ALA TYR M3L SER NH2 0.008032 0.4244 None
3 5EPL 5R0 PHE ALA LEU ELY 5R5 0.008082 0.42286 None
4 3W6C NAG NAG 0.01678 0.42829 3.37079
5 2FZW NAD 0.04824 0.41904 3.37079
6 4R0M FA5 0.0153 0.41766 4.49438
7 2PZM UDP 0.001885 0.4777 5.61798
8 2PZM NAD 0.001885 0.4777 5.61798
9 1M0W 3GC 0.01496 0.40313 5.61798
10 1WPQ NAD 0.04357 0.40256 5.61798
11 4ZTE 4RL 0.008757 0.4343 6.74157
12 2JFN UMA 0.02048 0.40777 6.74157
13 1SL3 170 0.02792 0.40165 6.74157
14 1ULM NAG NAG NAG 0.003494 0.44656 7.31707
15 3OV6 MK0 0.01042 0.43563 7.86517
16 3JWH SAH 0.01985 0.40557 7.86517
17 2G30 ALA ALA PHE 0.003524 0.44222 8.98876
18 3MKK GLC BGC 0.007409 0.41545 8.98876
19 4J1Q NDP 0.004985 0.43479 10.1124
20 1Z6Z NAP 0.04509 0.40391 12.3596
21 3UKR CKH 0.0003946 0.47377 13.4831
22 4JAW NGT GAL 0.01085 0.4129 13.4831
23 1EN2 NAG NAG NAG NAG 0.0015 0.45696 14.6067
24 1EHH NAG NAG NAG 0.001895 0.40467 14.6067
25 5ACM MBT 0.005929 0.42642 15.7303
26 5J75 6GQ 0.008913 0.43246 19.1011
27 3CH6 311 0.02874 0.42534 19.1011
28 3CH6 NAP 0.02874 0.42534 19.1011
29 1MEX RAC 0.02379 0.40536 30.3371
30 5GRF CIT 0.0134 0.40593 33.7079
Pocket No.: 4; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found: 60
This union binding pocket(no: 4) in the query (biounit: 4yef.bio7) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5L83 ASP TRP GLU ILE VAL 0.001155 0.4707 None
2 5E6O TRP GLU GLU LEU 0.003598 0.45584 None
3 3IWD M2T 0.01766 0.42331 None
4 1HGX 5GP 0.01733 0.42028 None
5 4K55 H6P 0.03016 0.41895 None
6 3F5A SIA GAL NAG 0.01061 0.41827 None
7 4OVZ P85 0.02227 0.41592 None
8 3R5J ACE ALA ASP VAL ALA ASA 0.006406 0.41547 None
9 1KQR MNA 0.01726 0.41461 None
10 2BOS GLA GAL GLC NBU 0.04205 0.41194 None
11 4AGQ P96 0.01176 0.40678 None
12 1RZX ACE VAL LYS GLU SER LEU VAL 0.04352 0.4037 None
13 2P3I MNA 0.02844 0.40038 None
14 2VDF OCT 0.001421 0.47778 2.24719
15 2GUD BMA 0.01656 0.42128 2.24719
16 1DQN IMU 0.02343 0.41342 2.24719
17 2R0D 4IP 0.04763 0.40092 2.24719
18 2Z9I GLY ALA THR VAL 0.01636 0.43149 3.37079
19 3LJU IP9 0.01571 0.41711 3.37079
20 5ARK UMP 0.03934 0.40543 3.37079
21 4KJU 1RH 0.03483 0.40897 3.48837
22 2BVE PH5 0.01063 0.43348 4.49438
23 2ZX2 RAM 0.01688 0.42938 4.49438
24 1SS4 GSH 0.0001499 0.47916 5.61798
25 4BS0 6NT 0.02746 0.4098 5.61798
26 2W5P CL8 0.03622 0.40941 5.61798
27 5GJH SER ASP PTR MET ASN MET THR PRO 0.02634 0.40691 5.61798
28 1MJT ITU 0.04643 0.40044 5.61798
29 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.03556 0.40022 5.61798
30 5KJW 53C 0.008331 0.44308 6.74157
31 3T4L ZEA 0.01225 0.40918 6.74157
32 4RT1 C2E 0.01446 0.40914 6.74157
33 3JU6 ANP 0.03627 0.40735 6.74157
34 2DT9 THR 0.04182 0.40017 6.74157
35 4JLS 3ZE 0.02975 0.41249 7.86517
36 4JMO JAF 0.02842 0.40901 7.86517
37 3GNE FLC 0.04027 0.40488 7.86517
38 4RDL FUC GAL NDG FUC 0.04496 0.40249 7.86517
39 5D9G GLU ASN LEU TYR PHE GLN 0.01763 0.4199 8.98876
40 4C2C ALA ALA ALA 0.04503 0.40059 8.98876
41 3ALN ANP 0.01645 0.40647 10.1124
42 3R4S SLB 0.03642 0.40984 11.236
43 2YKL NLD 0.02864 0.40149 11.236
44 5F6U 5VK 0.001618 0.48006 12.3596
45 1I1E DM2 0.01799 0.42375 12.3596
46 3JQ3 ADP 0.02083 0.41214 12.3596
47 5M6N 7H9 0.02986 0.41192 12.3596
48 4KBA 1QM 0.004015 0.45336 13.4831
49 1GPM AMP 0.01482 0.41826 13.4831
50 1GPM CIT 0.02845 0.41457 13.4831
51 1GG6 APL 0.03474 0.41137 13.4831
52 2WBV SIA 0.004936 0.44347 14.6067
53 3CM2 X23 0.03549 0.41081 15.7303
54 1XXR MAN 0.02849 0.4029 16.8539
55 3FIU AMP 0.02456 0.40848 20.2247
56 2PNC CLU 0.03925 0.40447 20.2247
57 2XG5 EC5 0.000691 0.50546 21.3483
58 2XG5 EC2 0.000691 0.50546 21.3483
59 3A16 PXO 0.01939 0.40362 22.4719
60 1PVC ILE SER GLU VAL 0.00775 0.43571 25.8427
Pocket No.: 5; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found: 2
This union binding pocket(no: 5) in the query (biounit: 4yef.bio6) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3G08 FEE 0.02587 0.42147 6.74157
2 1GQG DCD 0.002733 0.47034 13.4831
Pocket No.: 6; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found: 8
This union binding pocket(no: 6) in the query (biounit: 4yef.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1I82 BGC BGC 0.001329 0.43709 2.24719
2 2P1C GG3 0.03949 0.40303 2.24719
3 5V3Y 5V8 0.01409 0.41477 6.74157
4 1RX0 FAD 0.01904 0.43098 10.1124
5 2PD4 DCN 0.01916 0.42881 14.6067
6 2PD4 NAD 0.01909 0.42762 14.6067
7 1NFQ NAI 0.01856 0.41883 17.9775
8 3OZG SSI 0.01483 0.40501 23.5955
Pocket No.: 7; Query (leader) PDB : 4YEF; Ligand: 4CQ; Similar sites found: 1
This union binding pocket(no: 7) in the query (biounit: 4yef.bio3) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1N62 FAD 0.02772 0.40178 13.4831
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