NPASS Compound

Natural Product: NPC300557

Natural Product ID	NPC300557
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Gracillin
IUPAC Name	n.a.
Synonyms	Gracillin
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL500045
PubChem CID	159861
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides [CHEMONTID:0002364] Steroidal saponins

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 134142 0 0 0 0 0 0 0 0999 V2000 -6.7725 -2.3388 -4.7092 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5687 -1.6253 -4.5690 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2346 -1.6366 -3.0909 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0671 -0.9433 -2.9293 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6411 -0.8501 -1.5817 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4165 -0.2752 -1.5250 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3957 -1.0212 -1.0380 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2899 -1.3189 -2.0157 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6298 -0.1273 -2.2599 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4427 0.1224 -1.0289 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7071 -0.4691 0.1496 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3346 -1.1021 1.1161 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7911 -1.3245 1.1927 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5204 -0.4468 0.2139 C 0 0 2 0 0 0 0 0 0 0 0 0 2.8121 -0.5026 -1.1237 C 0 0 2 0 0 0 0 0 0 0 0 0 3.5693 -0.0161 -2.2917 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0497 -0.1635 -2.2729 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6016 0.0952 -0.9023 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9183 -0.9284 -0.0268 C 0 0 1 0 0 0 0 0 0 0 0 0 5.8066 -0.9416 1.1732 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1616 -1.1129 0.5158 C 0 0 1 0 0 0 0 0 0 0 0 0 7.0421 -0.3058 -0.7539 C 0 0 2 0 0 0 0 0 0 0 0 0 7.9945 0.8207 -0.5149 C 0 0 2 0 0 0 0 0 0 0 0 0 8.7228 1.2588 -1.7656 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0251 0.1051 0.3739 C 0 0 2 0 0 0 0 0 0 0 0 0 8.2082 -0.5994 1.2539 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7795 1.1311 1.1424 C 0 0 0 0 0 0 0 0 0 0 0 0 11.1849 1.3564 0.6670 C 0 0 0 0 0 0 0 0 0 0 0 0 11.8933 0.1334 0.1891 C 0 0 2 0 0 0 0 0 0 0 0 0 10.9885 -1.0562 0.3416 C 0 0 0 0 0 0 0 0 0 0 0 0 9.8125 -0.7650 -0.3644 O 0 0 0 0 0 0 0 0 0 0 0 0 13.2045 -0.1052 0.9340 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4032 1.5093 -0.4749 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7681 -0.3233 0.1524 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5308 1.5981 -0.7778 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7613 -0.0887 -0.8860 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9192 -1.0643 -0.8515 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.4112 -1.0619 -2.2876 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.4865 -1.8739 -2.5037 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8049 -0.7087 0.0904 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.0257 -1.6124 1.1152 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.3411 -2.0290 0.9076 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.7614 -3.0538 1.7377 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.2531 -3.2173 1.4089 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.8798 -2.0022 1.6937 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6868 -2.6893 3.1926 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.3111 -2.1834 3.4664 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9222 -1.0874 2.4970 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.6297 -0.7364 2.8808 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2325 -1.6994 4.7755 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.8804 -3.8142 3.9824 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4353 0.4751 0.3057 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4528 1.8668 0.2528 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2171 2.3901 0.5361 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0971 3.7211 0.2467 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1805 4.0158 -1.2382 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0730 4.5683 1.0319 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.8449 3.6741 1.9525 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.4496 2.4924 1.2041 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.5118 3.0396 0.4532 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8642 4.4200 2.5264 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4113 5.5157 1.8243 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7035 -3.0335 -5.3983 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7639 -2.0685 -5.1647 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6765 -0.5618 -4.8638 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0946 -2.6710 -2.7026 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6838 -1.8951 -1.2124 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8026 -2.0125 -0.7392 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6203 -1.7809 -2.9444 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3670 -2.0806 -1.5110 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2463 -0.4127 -3.1314 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0547 0.7624 -2.5882 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7406 -1.5230 1.9726 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0620 -2.3983 1.0544 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1610 -1.0293 2.2252 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5163 0.5776 0.6402 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6150 -1.6086 -1.2788 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2271 -0.6248 -3.1920 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3509 1.0257 -2.6085 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5070 0.5518 -2.9742 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3389 -1.1929 -2.5780 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9085 -1.9008 -0.5122 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6287 -1.8463 1.7939 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8079 -0.0045 1.7378 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3348 -2.1890 0.2242 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3861 -0.8782 -1.6492 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6163 1.6468 0.0847 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2918 2.1913 -1.4922 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4716 0.5235 -2.1005 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0437 1.5356 -2.5872 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7878 0.8565 2.2355 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2456 2.1155 1.0993 H 0 0 0 0 0 0 0 0 0 0 0 0 11.2575 2.1931 -0.0883 H 0 0 0 0 0 0 0 0 0 0 0 0 11.7685 1.7509 1.5500 H 0 0 0 0 0 0 0 0 0 0 0 0 12.1483 0.2594 -0.8830 H 0 0 0 0 0 0 0 0 0 0 0 0 11.4456 -1.9764 -0.0239 H 0 0 0 0 0 0 0 0 0 0 0 0 10.7432 -1.1459 1.4372 H 0 0 0 0 0 0 0 0 0 0 0 0 13.4034 -1.1980 0.9008 H 0 0 0 0 0 0 0 0 0 0 0 0 13.1312 0.1881 1.9865 H 0 0 0 0 0 0 0 0 0 0 0 0 14.0316 0.3799 0.3985 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0695 2.1312 -1.1444 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3998 1.9003 -0.6436 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6411 1.6699 0.5883 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2214 -0.7076 1.0930 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0346 0.7759 0.1516 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1274 2.1684 -1.5046 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5048 2.0636 -0.8283 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8508 1.8210 0.2831 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9870 0.7562 -1.6178 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4500 -2.0725 -0.6366 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6087 -0.0276 -2.5835 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2301 -1.3209 -2.8929 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3956 -2.5409 0.9895 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2697 -4.0044 1.5325 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.3715 -3.3490 0.2950 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.7434 -3.9988 1.9780 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.3648 -1.2271 1.3273 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.4114 -1.8810 3.4052 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5593 -3.0091 3.3234 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6371 -0.2600 2.6274 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9868 -1.2912 2.3757 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4290 -2.3973 5.4408 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.6193 -4.3507 3.6091 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7187 2.1686 -0.8028 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0690 4.0315 0.5708 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7173 3.1688 -1.7583 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5642 4.9151 -1.4414 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2236 4.2272 -1.5577 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7078 5.1363 0.3286 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1712 3.3480 2.7636 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8863 1.7963 1.9138 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3740 2.9103 0.8771 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6303 5.3998 2.5457 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6407 6.4359 1.5726 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 23 25 1 0 25 26 1 1 25 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 29 32 1 0 18 33 1 1 11 34 1 0 10 35 1 1 5 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 37 40 1 0 40 41 1 0 41 42 1 0 42 43 1 0 43 44 1 0 44 45 1 0 43 46 1 0 46 47 1 0 47 48 1 0 48 49 1 0 47 50 1 0 46 51 1 0 36 52 1 0 52 53 1 0 53 54 1 0 54 55 1 0 55 56 1 0 55 57 1 0 57 58 1 0 58 59 1 0 59 60 1 0 58 61 1 0 57 62 1 0 38 3 1 0 48 41 1 0 59 53 1 0 34 7 1 0 15 10 1 0 22 18 1 0 31 25 1 0 19 14 1 0 26 21 1 0 1 63 1 0 2 64 1 0 2 65 1 0 3 66 1 1 5 67 1 1 7 68 1 1 8 69 1 0 8 70 1 0 9 71 1 0 9 72 1 0 12 73 1 0 13 74 1 0 13 75 1 0 14 76 1 1 15 77 1 6 16 78 1 0 16 79 1 0 17 80 1 0 17 81 1 0 19 82 1 6 20 83 1 0 20 84 1 0 21 85 1 6 22 86 1 6 23 87 1 1 24 88 1 0 24 89 1 0 24 90 1 0 27 91 1 0 27 92 1 0 28 93 1 0 28 94 1 0 29 95 1 6 30 96 1 0 30 97 1 0 32 98 1 0 32 99 1 0 32100 1 0 33101 1 0 33102 1 0 33103 1 0 34104 1 0 34105 1 0 35106 1 0 35107 1 0 35108 1 0 36109 1 6 37110 1 1 38111 1 6 39112 1 0 41113 1 1 43114 1 1 44115 1 0 44116 1 0 45117 1 0 46118 1 1 47119 1 1 48120 1 6 49121 1 0 50122 1 0 51123 1 0 53124 1 6 55125 1 1 56126 1 0 56127 1 0 56128 1 0 57129 1 6 58130 1 1 59131 1 1 60132 1 0 61133 1 0 62134 1 0 M END

Standard InCHIKey	YQEMAEKYNNOCBY-IEMDQPGHSA-N
Standard InCHI	InChI=1S/C45H72O17/c1-19-8-13-45(55-18-19)20(2)30-27(62-45)15-26-24-7-6-22-14-23(9-11-43(22,4)25(24)10-12-44(26,30)5)57-42-39(61-40-36(53)34(51)31(48)21(3)56-40)38(33(50)29(17-47)59-42)60-41-37(54)35(52)32(49)28(16-46)58-41/h6,19-21,23-42,46-54H,7-18H2,1-5H3/t19-,20+,21+,23+,24-,25+,26+,27+,28-,29-,30+,31+,32-,33-,34-,35+,36-,37-,38+,39-,40+,41+,42-,43+,44+,45-/m1/s1
SMILES	OC[C@H]1O[C@@H](O[C@H]2CC[C@]3(C(=CC[C@@H]4[C@@H]3CC[C@]3([C@H]4C[C@H]4[C@@H]3[C@H](C)[C@]3(O4)CC[C@H](CO3)C)C)C2)C)[C@@H]([C@H]([C@@H]1O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	884.48	Volume:	856.665 ? Van der Waals volume.
Dense:	1.032	LogP:	2.373 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.178 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.683 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	48.0
TPSA:	255.91 ? Topological Polar Surface Area.	H-Bond Acceptor:	17.0
H-Bond Donor:	9.0	Rings:	9.0
Heavy Atoms:	17.0

MedChem Properties

QED Drug-Likeness Score:	0.148	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.687	Fsp³:	0.956
MCE-18:	229.091 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.739	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.004 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.234	Promiscuous compounds:	0.012

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.246	MDCK Permeability:	-5.11
Pgp-inhibitor:	0.0	Pgp-substrate:	0.745
PAMPA:	0.994 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.0
20% Bioavailability (F20%):	0.007	30% Bioavailability (F30%):	0.799
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002	MRP1:	0.004
Plasma Protein Binding (PPB):	63.546%	Volume Distribution (VD):	-0.409
Fu:	28.834% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.593
BSEP inhibitor:	0.025

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.012	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.001
CYP3A4-inhibitor:	0.999	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.982
HLM stability:	0.93 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

0.419

Half-life (T1/2):

3.29

ADMET: Toxicity

hERG Blockers:	0.025	hERG Blockers (10um):	0.059
Human Hepatotoxicity (H-HT):	0.405	Drug-induced Liver Injury (DILI):	0.974
AMES Toxicity:	0.908	Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.007	Skin Sensitization:	1.0
Carcinogencity:	0.061	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.999
Hematotoxicity:	0.128	Drug-induced Nephrotoxicity:	0.736
Genotoxicity:	0.004	RPMI-8226 Immunitoxicity:	0.27
A549 Cytotoxicity:	0.802	Hek293 Cytotoxicity:	0.841
BCF:	1.741 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	3.39 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.577 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.958 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO7395	Tribulus terrestris	Species	Zygophyllaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[11141122]
NPO3545	Dracaena draco	Species	Asparagaceae	Eukaryota	bark	n.a.	n.a.	PMID[12828464]
NPO19123	Polygonatum zanlanscianense	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15620239]
NPO14409	Dioscorea nipponica	Species	Dioscoreaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[23707257]
NPO19123	Polygonatum zanlanscianense	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3545	Dracaena draco	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO127	Phragmites australis	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15886	Lepidium campestre	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9089	Dioscorea panthaica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27472	Daiswa polyphylla	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7395	Tribulus terrestris	Species	Zygophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14409	Dioscorea nipponica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15886	Lepidium campestre	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14409	Dioscorea nipponica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7395	Tribulus terrestris	Species	Zygophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9089	Dioscorea panthaica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3545	Dracaena draco	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19123	Polygonatum zanlanscianense	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO127	Phragmites australis	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19123	Polygonatum zanlanscianense	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3545	Dracaena draco	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9089	Dioscorea panthaica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14409	Dioscorea nipponica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27472	Daiswa polyphylla	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15886	Lepidium campestre	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7395	Tribulus terrestris	Species	Zygophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7395	Tribulus terrestris	Species	Zygophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3545	Dracaena draco	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14409	Dioscorea nipponica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9089	Dioscorea panthaica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO7395	Tribulus terrestris	Species	Zygophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27472	Daiswa polyphylla	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO127	Phragmites australis	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14409	Dioscorea nipponica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9089	Dioscorea panthaica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19123	Polygonatum zanlanscianense	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15886	Lepidium campestre	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14409	Dioscorea nipponica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27472	Daiswa polyphylla	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19342	Bryocladia cuspidata	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20313	Crotalus mitchellii	Species	Viperidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3545	Dracaena draco	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO127	Phragmites australis	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7802	Dacrycarpus vieillardii	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7395	Tribulus terrestris	Species	Zygophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
IC50	11

Activity Type	# Activity
Cell line	11

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT165	Cell line	HeLa	Homo sapiens	IC50	=	12.74	ug.mL-1	PMID[15620239]
NPT116	Cell line	HL-60	Homo sapiens	IC50	=	3700.0	nM	PMID[12828464]
NPT1312	Cell line	SW1990	Homo sapiens	IC50	=	1100.0	nM	PMID[19362474]
NPT1081	Cell line	BXPC-3	Homo sapiens	IC50	=	1300.0	nM	PMID[19362474]
NPT1313	Cell line	Capan-2	Homo sapiens	IC50	=	1300.0	nM	PMID[19362474]
NPT461	Cell line	PANC-1	Homo sapiens	IC50	=	700.0	nM	PMID[19362474]
NPT81	Cell line	A549	Homo sapiens	IC50	=	960.0	nM	PMID[19362474]
NPT181	Cell line	Bel-7402	Homo sapiens	IC50	=	1100.0	nM	PMID[19362474]
NPT179	Cell line	A2780	Homo sapiens	IC50	=	4300.0	nM	PMID[19362474]
NPT180	Cell line	HCT-8	Homo sapiens	IC50	=	920.0	nM	PMID[19362474]
NPT83	Cell line	MCF7	Homo sapiens	IC50	=	17500.0	nM	PMID[19362474]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC300557 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	24189
0.1-0.2	22055
0.2-0.3	2722
0.3-0.4	625
0.4-0.5	96
0.5-0.6	84
0.6-0.7	49
0.7-0.8	0
0.8-0.85	7
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9775	High Similarity	NPC602423
0.8866	High Similarity	NPC309278
0.8265	Intermediate Similarity	NPC480555
0.8265	Intermediate Similarity	NPC150372
0.8211	Intermediate Similarity	NPC113044
0.8211	Intermediate Similarity	NPC283829
0.8211	Intermediate Similarity	NPC161676
0.8155	Intermediate Similarity	NPC477811
0.8	Intermediate Similarity	NPC181845
0.7959	Intermediate Similarity	NPC470433
0.7959	Intermediate Similarity	NPC46190
0.7959	Intermediate Similarity	NPC171073
0.7835	Intermediate Similarity	NPC14704
0.7812	Intermediate Similarity	NPC470432
0.7812	Intermediate Similarity	NPC230507
0.781	Intermediate Similarity	NPC480553
0.7798	Intermediate Similarity	NPC477808
0.7619	Intermediate Similarity	NPC480554
0.7579	Intermediate Similarity	NPC206003
0.7579	Intermediate Similarity	NPC473610
0.75	Intermediate Similarity	NPC269297
0.75	Intermediate Similarity	NPC222202
0.7429	Intermediate Similarity	NPC475333
0.7429	Intermediate Similarity	NPC224098
0.7429	Intermediate Similarity	NPC208383
0.7358	Intermediate Similarity	NPC194207
0.7358	Intermediate Similarity	NPC22779
0.7353	Intermediate Similarity	NPC248746
0.7353	Intermediate Similarity	NPC477809
0.7308	Intermediate Similarity	NPC102016
0.7308	Intermediate Similarity	NPC95051
0.7282	Intermediate Similarity	NPC6806
0.7248	Intermediate Similarity	NPC31896
0.7143	Intermediate Similarity	NPC480556
0.7059	Intermediate Similarity	NPC475351
0.7027	Intermediate Similarity	NPC232054
0.6972	Remote Similarity	NPC218571
0.6972	Remote Similarity	NPC487615
0.6952	Remote Similarity	NPC42171
0.6887	Remote Similarity	NPC150057
0.6887	Remote Similarity	NPC147753
0.681	Remote Similarity	NPC210569
0.6789	Remote Similarity	NPC13193
0.6783	Remote Similarity	NPC224314
0.6765	Remote Similarity	NPC125324
0.6699	Remote Similarity	NPC141433
0.6638	Remote Similarity	NPC477807
0.6635	Remote Similarity	NPC305423
0.6514	Remote Similarity	NPC97700
0.6514	Remote Similarity	NPC184617
0.6514	Remote Similarity	NPC30856
0.65	Remote Similarity	NPC305771
0.65	Remote Similarity	NPC94072
0.65	Remote Similarity	NPC169816
0.6486	Remote Similarity	NPC32361
0.6442	Remote Similarity	NPC6295
0.6396	Remote Similarity	NPC475550
0.6355	Remote Similarity	NPC473601
0.6337	Remote Similarity	NPC477451
0.633	Remote Similarity	NPC51172
0.633	Remote Similarity	NPC49032
0.6316	Remote Similarity	NPC83137
0.6263	Remote Similarity	NPC485594
0.625	Remote Similarity	NPC15918
0.623	Remote Similarity	NPC263359
0.6204	Remote Similarity	NPC40440
0.6182	Remote Similarity	NPC48886
0.6182	Remote Similarity	NPC94881
0.6161	Remote Similarity	NPC475319
0.6154	Remote Similarity	NPC19400
0.6139	Remote Similarity	NPC297348
0.6139	Remote Similarity	NPC249204
0.6139	Remote Similarity	NPC48339
0.6139	Remote Similarity	NPC141769
0.6139	Remote Similarity	NPC477547
0.6126	Remote Similarity	NPC475182
0.6121	Remote Similarity	NPC132080
0.6071	Remote Similarity	NPC73243
0.6071	Remote Similarity	NPC244086
0.6071	Remote Similarity	NPC84956
0.6055	Remote Similarity	NPC98696
0.6036	Remote Similarity	NPC124677
0.6018	Remote Similarity	NPC115165
0.6	Remote Similarity	NPC306131
0.6	Remote Similarity	NPC200802
0.5981	Remote Similarity	NPC94272
0.5981	Remote Similarity	NPC485595
0.598	Remote Similarity	NPC325828
0.5968	Remote Similarity	NPC244431
0.5965	Remote Similarity	NPC247037
0.5929	Remote Similarity	NPC294129
0.5922	Remote Similarity	NPC234352
0.5913	Remote Similarity	NPC116756
0.5909	Remote Similarity	NPC42482
0.5872	Remote Similarity	NPC160426
0.5862	Remote Similarity	NPC232037
0.5812	Remote Similarity	NPC249265
0.5812	Remote Similarity	NPC470864
0.5789	Remote Similarity	NPC100451
0.578	Remote Similarity	NPC195297
0.578	Remote Similarity	NPC70204
0.5776	Remote Similarity	NPC473518
0.5763	Remote Similarity	NPC23808
0.5763	Remote Similarity	NPC87998
0.5752	Remote Similarity	NPC249553
0.5752	Remote Similarity	NPC182900
0.5741	Remote Similarity	NPC107962
0.5726	Remote Similarity	NPC79900
0.5714	Remote Similarity	NPC233433
0.5714	Remote Similarity	NPC469347
0.5702	Remote Similarity	NPC151134
0.5701	Remote Similarity	NPC211354
0.5701	Remote Similarity	NPC107188
0.566	Remote Similarity	NPC222731
0.563	Remote Similarity	NPC476112
0.563	Remote Similarity	NPC307534
0.5579	Remote Similarity	NPC235126
0.5579	Remote Similarity	NPC242419
0.5574	Remote Similarity	NPC470866
0.5565	Remote Similarity	NPC128572
0.5546	Remote Similarity	NPC108072
0.5537	Remote Similarity	NPC308140
0.5492	Remote Similarity	NPC167183
0.5481	Remote Similarity	NPC481189
0.5472	Remote Similarity	NPC294686
0.5462	Remote Similarity	NPC232611
0.5446	Remote Similarity	NPC277715
0.5397	Remote Similarity	NPC220836
0.5391	Remote Similarity	NPC122819
0.5373	Remote Similarity	NPC329807
0.5372	Remote Similarity	NPC470862
0.5351	Remote Similarity	NPC486388
0.5347	Remote Similarity	NPC144790
0.5347	Remote Similarity	NPC149400
0.5304	Remote Similarity	NPC475643
0.5294	Remote Similarity	NPC486386
0.5268	Remote Similarity	NPC15249
0.5268	Remote Similarity	NPC306991
0.5268	Remote Similarity	NPC25455
0.5254	Remote Similarity	NPC475247
0.5229	Remote Similarity	NPC250393
0.5217	Remote Similarity	NPC329727
0.5214	Remote Similarity	NPC471464
0.5207	Remote Similarity	NPC254255
0.5194	Remote Similarity	NPC32707
0.5189	Remote Similarity	NPC165439
0.5188	Remote Similarity	NPC481190
0.5179	Remote Similarity	NPC295980
0.5159	Remote Similarity	NPC94086
0.5159	Remote Similarity	NPC473817
0.5152	Remote Similarity	NPC486119
0.5143	Remote Similarity	NPC24960
0.5124	Remote Similarity	NPC475625
0.5118	Remote Similarity	NPC248202
0.5088	Remote Similarity	NPC475670
0.5086	Remote Similarity	NPC161738
0.5081	Remote Similarity	NPC256983
0.5078	Remote Similarity	NPC473505
0.5072	Remote Similarity	NPC329820
0.5048	Remote Similarity	NPC481420
0.5048	Remote Similarity	NPC473774
0.5048	Remote Similarity	NPC481419
0.5048	Remote Similarity	NPC481417
0.5048	Remote Similarity	NPC481421
0.5046	Remote Similarity	NPC131693
0.5046	Remote Similarity	NPC475436
0.5043	Remote Similarity	NPC470748
0.504	Remote Similarity	NPC287885
0.5037	Remote Similarity	NPC330026

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC300557 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7613
0.1-0.2	1444
0.2-0.3	82
0.3-0.4	5
0.4-0.5	2
0.5-0.6	3
0.6-0.7	1
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6887	Remote Similarity	NPD8450	Suspended
0.598	Remote Similarity	NPD8171	Phase 2
0.5405	Remote Similarity	NPD8170	Phase 2
0.5391	Remote Similarity	NPD8449	Approved

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data