Receptor
PDB id Resolution Class Description Source Keywords
2AGC 2.5 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF MOUSE GM2- ACTIVATOR PROTEIN MUS MUSCULUS CONSTRICTED LIPID BINDING POCKET LIPID BINDING PROTEIN
Ref.: CRYSTAL STRUCTURE ANALYSIS OF PHOSPHATIDYLCHOLINE-GM2-ACTIVATOR PRODUCT COMPLEXES: EVIDENCE FOR HYDROLASE ACTIVITY. BIOCHEMISTRY V. 44 13510 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DAO A:2055;
A:2057;
Valid;
Valid;
none;
none;
submit data
200.318 C12 H24 O2 CCCCC...
MYR A:3045;
Valid;
none;
submit data
228.371 C14 H28 O2 CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2AGC 2.5 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF MOUSE GM2- ACTIVATOR PROTEIN MUS MUSCULUS CONSTRICTED LIPID BINDING POCKET LIPID BINDING PROTEIN
Ref.: CRYSTAL STRUCTURE ANALYSIS OF PHOSPHATIDYLCHOLINE-GM2-ACTIVATOR PRODUCT COMPLEXES: EVIDENCE FOR HYDROLASE ACTIVITY. BIOCHEMISTRY V. 44 13510 2005
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 families.
1 2AGC - MYR C14 H28 O2 CCCCCCCCCC....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 196 families.
1 2AG4 - LP3 C26 H55 N O7 P CCCCCCCCCC....
2 1TJJ - DAO C12 H24 O2 CCCCCCCCCC....
3 2AG9 - MYR C14 H28 O2 CCCCCCCCCC....
4 2AF9 - MYR C14 H28 O2 CCCCCCCCCC....
5 2AG2 - DAO C12 H24 O2 CCCCCCCCCC....
6 2AGC - MYR C14 H28 O2 CCCCCCCCCC....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 171 families.
1 2AG4 - LP3 C26 H55 N O7 P CCCCCCCCCC....
2 1TJJ - DAO C12 H24 O2 CCCCCCCCCC....
3 2AG9 - MYR C14 H28 O2 CCCCCCCCCC....
4 2AF9 - MYR C14 H28 O2 CCCCCCCCCC....
5 2AG2 - DAO C12 H24 O2 CCCCCCCCCC....
6 2AGC - MYR C14 H28 O2 CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DAO; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 F23 1 1
3 11A 1 1
4 STE 1 1
5 KNA 1 1
6 TDA 1 1
7 DCR 1 1
8 DAO 1 1
9 DKA 1 1
10 PLM 1 1
11 F15 1 1
12 OCA 0.956522 1
13 SHV 0.833333 0.952381
14 KTC 0.793103 0.875
15 AZ1 0.73913 0.64
16 6NA 0.72 0.904762
17 NER 0.71875 0.954545
18 OLA 0.71875 0.954545
19 ELA 0.71875 0.954545
20 VCA 0.666667 0.954545
21 PAM 0.666667 0.954545
22 PML 0.625 0.6
23 3LA 0.606061 0.8
24 LEA 0.6 0.809524
25 MYZ 0.588235 0.909091
26 12H 0.586207 0.615385
27 ODD 0.567568 0.913043
28 BRC 0.566667 0.666667
29 14V 0.555556 0.740741
30 M12 0.545455 0.869565
31 14U 0.542857 0.703704
32 EIC 0.538462 0.913043
33 EOD 0.538462 0.7
34 BUA 0.48 0.666667
35 RCL 0.468085 0.84
36 HXD 0.459459 0.807692
37 56S 0.459459 0.653846
38 ODT 0.452381 0.782609
39 3X1 0.444444 0.818182
40 LNL 0.44186 0.826087
41 CNS 0.435897 0.68
42 6UL 0.435897 0.68
43 5UF 0.432432 0.807692
44 243 0.428571 0.807692
45 GYM 0.418605 0.606061
46 PL3 0.413793 0.75
47 O8N 0.413793 0.75
48 1DO 0.413793 0.75
49 F09 0.413793 0.75
50 OC9 0.413793 0.75
51 DE1 0.413793 0.75
52 T25 0.403846 0.677419
Ligand no: 2; Ligand: MYR; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 F23 1 1
3 11A 1 1
4 STE 1 1
5 KNA 1 1
6 TDA 1 1
7 DCR 1 1
8 DAO 1 1
9 DKA 1 1
10 PLM 1 1
11 F15 1 1
12 OCA 0.956522 1
13 SHV 0.833333 0.952381
14 KTC 0.793103 0.875
15 AZ1 0.73913 0.64
16 6NA 0.72 0.904762
17 NER 0.71875 0.954545
18 OLA 0.71875 0.954545
19 ELA 0.71875 0.954545
20 VCA 0.666667 0.954545
21 PAM 0.666667 0.954545
22 PML 0.625 0.6
23 3LA 0.606061 0.8
24 LEA 0.6 0.809524
25 MYZ 0.588235 0.909091
26 12H 0.586207 0.615385
27 ODD 0.567568 0.913043
28 BRC 0.566667 0.666667
29 14V 0.555556 0.740741
30 M12 0.545455 0.869565
31 14U 0.542857 0.703704
32 EIC 0.538462 0.913043
33 EOD 0.538462 0.7
34 BUA 0.48 0.666667
35 RCL 0.468085 0.84
36 HXD 0.459459 0.807692
37 56S 0.459459 0.653846
38 ODT 0.452381 0.782609
39 3X1 0.444444 0.818182
40 LNL 0.44186 0.826087
41 CNS 0.435897 0.68
42 6UL 0.435897 0.68
43 5UF 0.432432 0.807692
44 243 0.428571 0.807692
45 GYM 0.418605 0.606061
46 PL3 0.413793 0.75
47 O8N 0.413793 0.75
48 1DO 0.413793 0.75
49 F09 0.413793 0.75
50 OC9 0.413793 0.75
51 DE1 0.413793 0.75
52 T25 0.403846 0.677419
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2AGC; Ligand: DAO; Similar sites found: 141
This union binding pocket(no: 1) in the query (biounit: 2agc.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2E56 MYR 0.004068 0.45175 None
2 3NW7 LGV 0.01686 0.43297 None
3 4PSB GA3 0.01733 0.42257 None
4 4R38 RBF 0.006631 0.42696 1.42857
5 3WG3 A2G GAL NAG FUC 0.001754 0.42294 1.85185
6 4YGF AZM 0.0005442 0.41067 1.85185
7 4WVW SLT 0.001351 0.45214 2.08333
8 4HIA FMN 0.004033 0.45698 2.46914
9 4X5S AZM 0.001244 0.45548 2.46914
10 2YG2 S1P 0.002634 0.45063 2.46914
11 3FW9 SLX 0.00232 0.44768 2.46914
12 5L6G XYP 0.004124 0.43611 2.46914
13 2YG2 FLC 0.01564 0.41614 2.46914
14 2Z6D FMN 0.004307 0.43438 3.07692
15 3FW3 ETS 0.0002629 0.4813 3.08642
16 1WUB OTP 0.00829 0.44778 3.08642
17 4RFR RHN 0.003023 0.44199 3.08642
18 2GQS ADP 0.002812 0.43931 3.08642
19 5J75 6GQ 0.002845 0.43905 3.08642
20 2AXR ABL 0.005606 0.42586 3.08642
21 4MLO PAM 0.005628 0.42236 3.08642
22 4I42 1HA 0.01648 0.41897 3.08642
23 3PQB VGP 0.01095 0.41783 3.08642
24 3MVH WFE 0.01996 0.41466 3.08642
25 3H7J PPY 0.009693 0.41085 3.08642
26 2ET1 GLV 0.004559 0.40379 3.08642
27 5JKG 6LF 0.04489 0.40367 3.08642
28 5LRT ADP 0.02873 0.40119 3.08642
29 3SAO NKN 0.00111 0.45661 3.125
30 1ULE GLA GAL NAG 0.001179 0.41788 3.33333
31 4QA8 PJZ 0.004415 0.44104 3.7037
32 2GQR ADP 0.003591 0.43411 3.7037
33 4YZC STU 0.01965 0.42184 3.7037
34 1AUA BOG 0.008558 0.41103 3.7037
35 5H2D ERG 0.01667 0.41026 3.7037
36 4IAW LIZ 0.005839 0.40529 3.7037
37 3I7V ATP 0.004566 0.4236 3.73134
38 5H9Q TD2 0.002296 0.44715 3.87097
39 2CM4 RCL 0.009067 0.42194 4
40 5ML3 DL3 0.01473 0.42953 4.02685
41 3PFG TLO 0.006286 0.45325 4.32099
42 4XIZ LPP 0.005817 0.44624 4.32099
43 2RG0 CTT 0.008829 0.43168 4.32099
44 4G7A AZM 0.001475 0.42631 4.32099
45 3M3R BCD 0.01932 0.42525 4.32099
46 1OJJ GLC GAL 0.004482 0.41965 4.32099
47 1OJK GLC BGC 0.004692 0.41871 4.32099
48 1ZM1 BGC BGC BGC 0.007944 0.41722 4.32099
49 4KYS VIB 0.004025 0.41575 4.32099
50 4P25 FUC GAL NAG FUC 0.01218 0.41009 4.32099
51 2RFZ CTR 0.01629 0.4057 4.32099
52 3LXK MI1 0.02731 0.40504 4.32099
53 1OGX EQU 0.01085 0.40846 4.58015
54 1URX AAL GAL AAL GLA 0.01039 0.40937 4.60993
55 4Q0L V14 0.0008511 0.47891 4.93827
56 4OMJ 2TX 0.01546 0.42405 4.93827
57 5VC5 96M 0.01434 0.41946 4.93827
58 5HES 032 0.01071 0.4183 4.93827
59 3W68 VIV 0.01229 0.41694 4.93827
60 4EIP FAD 0.04296 0.41165 4.93827
61 1VJ7 GDP 0.01306 0.40202 4.93827
62 1OLM VTQ 0.03318 0.40065 4.93827
63 4MNS 2AX 0.000689 0.51073 5.03145
64 1MDC PLM 0.006949 0.42944 5.30303
65 1T27 PCW 0.002672 0.4741 5.55556
66 4COQ SAN 0.0009312 0.46238 5.55556
67 5FQK 6NT 0.001295 0.45557 5.55556
68 5KEW 6SB 0.002677 0.43835 5.55556
69 3RGA LSB 0.00631 0.42212 5.55556
70 4V24 GYR 0.01702 0.42069 5.55556
71 1EHI ADP 0.009891 0.41647 5.55556
72 1ZB6 GST 0.02176 0.4127 5.55556
73 3THR C2F 0.01298 0.40675 5.55556
74 4IEN GDP 0.01415 0.40491 5.55556
75 2WA4 069 0.004675 0.40251 5.55556
76 2NAD NAD 0.04991 0.40022 5.55556
77 1FDQ HXA 0.006916 0.43714 6.10687
78 1J3R 6PG 0.001261 0.4487 6.17284
79 3ML5 AZM 0.001307 0.42809 6.17284
80 3NJV RAM GTR RAM GTR RAM GTR 0.02589 0.40056 6.17284
81 2A1L PCW 0.00187 0.48342 6.79012
82 2GC0 PAN 0.001692 0.45233 6.79012
83 4J7Q B7N 0.01491 0.41721 6.79012
84 2PYW ADP 0.01364 0.41132 6.79012
85 2X34 UQ8 0.02329 0.42619 7.40741
86 5FBN 5WF 0.02332 0.41577 7.40741
87 5UR1 YY9 0.02575 0.4101 7.40741
88 1GT4 UNA 0.008488 0.41581 7.54717
89 5T7I LAT NAG GAL 0.008438 0.41363 7.74194
90 1EWF PC1 0.006642 0.45097 8.02469
91 3WV6 GAL BGC 0.001421 0.43997 8.02469
92 2XK9 XK9 0.01098 0.43412 8.02469
93 5FL5 82E 0.005595 0.42016 8.02469
94 1GQG DCD 0.01247 0.41662 8.02469
95 2PUL ACP 0.01325 0.4063 8.02469
96 1PZO CBT 0.04656 0.40467 8.02469
97 4QDC ASD 0.008537 0.41568 8.64198
98 1Y0G 8PP 0.03552 0.4137 8.64198
99 2HZQ STR 0.009717 0.41123 8.64198
100 5ISY NAD 0.009163 0.40979 8.64198
101 3HX3 RET 0.01249 0.40955 8.64198
102 3VQ2 LP4 LP5 MYR DAO 0.01685 0.43122 9.02778
103 3L9R L9Q 0.04418 0.40105 9.18367
104 2X2M X2M 0.008866 0.42242 9.25926
105 5A3T MMK 0.01754 0.41881 9.25926
106 4P7X AKG 0.0183 0.40134 9.25926
107 2OVW CBI 0.0024 0.43805 9.87654
108 4B2Z P5S 0.01847 0.42531 9.87654
109 5IH9 6BF 0.02912 0.41173 9.87654
110 3AGC RCC 0.02851 0.40406 9.87654
111 3MTX PGT 0.003496 0.45648 9.93377
112 5DJT FMN 0.01965 0.40164 10.3448
113 1DMY AZM 0.0007704 0.45601 10.4938
114 4CLI 5P8 0.0376 0.41236 10.4938
115 3KOX Z98 0.01752 0.40412 10.7438
116 2WT2 GAL NAG GAL NAG GAL NAG 0.01103 0.42243 11.1111
117 1GP6 QUE 0.02082 0.40977 11.1111
118 1GP6 SIN 0.02327 0.40588 11.1111
119 5CJF 520 0.0008178 0.43638 11.7284
120 5LNE A2G GAL 0.01024 0.40493 11.7284
121 1GSA ADP 0.0217 0.40445 11.7284
122 4EES FMN 0.02074 0.4022 12.1739
123 4Y24 TD2 0.005989 0.41627 12.3377
124 1ODM ASV 0.01861 0.41085 12.3457
125 1MH5 HAL 0.02363 0.40554 12.3457
126 3KFF XBT 0.01213 0.40359 12.963
127 3E2M E2M 0.008417 0.42842 13.5802
128 4QCK ASD 0.01212 0.40613 13.5802
129 3OYW TDG 0.003208 0.41978 14.1791
130 1SQI 869 0.01325 0.40631 14.1975
131 2QL9 CIT 0.0005139 0.42086 14.433
132 5HCY 60D 0.01536 0.43339 14.8148
133 2QO4 CHD 0.01153 0.42701 15.0794
134 2X4Z X4Z 0.02363 0.41548 16.0494
135 4K55 H6P 0.0003072 0.41627 16.129
136 4USF 6UI 0.0008257 0.47779 16.6667
137 1ZHX HC3 0.005957 0.43758 17.9012
138 2Y6O 1N1 0.002125 0.45348 20.3704
139 2H8H H8H 0.01604 0.40418 21.6049
140 4OPC FDA 0.02709 0.44764 22.8395
141 2P7Q GG6 0.007106 0.40264 25.5639
Pocket No.: 2; Query (leader) PDB : 2AGC; Ligand: DAO; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2agc.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2AGC; Ligand: MYR; Similar sites found: 13
This union binding pocket(no: 3) in the query (biounit: 2agc.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2E56 MYR 0.002478 0.44955 None
2 2QZT PLM 0.01591 0.42542 None
3 2XMY CDK 0.01652 0.44643 1.85185
4 1WUB OTP 0.01102 0.44229 3.08642
5 5ML3 DL3 0.01734 0.42889 4.02685
6 3Q8G PEE 0.03064 0.41226 4.32099
7 4MNS 2AX 0.009107 0.43988 5.03145
8 1MZC BNE 0.04658 0.42187 8.02469
9 3VQ2 LP4 LP5 MYR DAO 0.002086 0.46993 9.02778
10 3DBX PLM 0.009146 0.4135 9.09091
11 3G08 FEE 0.02241 0.42057 11.7284
12 4OPC FDA 0.01309 0.44506 22.8395
13 4OPC PGT 0.01828 0.44139 22.8395
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