NPASS Compound

Natural Product: NPC49032

Natural Product ID	NPC49032
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	OKXQHXAEZMQAFY-NPOQUHPBSA-N
IUPAC Name	n.a.
Synonyms	schidigera-saponin A2
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL465585
PubChem CID	10819444
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 131139 0 0 0 0 0 0 0 0999 V2000 -5.4749 -3.1960 -5.1779 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6355 -2.1486 -4.8151 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4155 -2.0874 -3.3210 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5798 -1.0291 -3.0561 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3047 -0.9362 -1.6603 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3407 0.0145 -1.5376 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1521 -0.4697 -0.9712 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0538 -0.4999 -2.0199 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7681 0.7402 -2.0404 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3814 1.1027 -0.7068 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6819 0.4810 0.4520 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8116 0.3769 0.2010 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1629 -0.8558 0.8841 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5150 -1.2603 0.3721 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3692 0.0159 0.3892 C 0 0 2 0 0 0 0 0 0 0 0 0 2.8473 0.8415 -0.7793 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6695 2.1021 -0.9301 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1253 1.7763 -1.1023 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6218 0.9178 0.0086 C 0 0 1 0 0 0 0 0 0 0 0 0 4.7783 -0.3265 0.0566 C 0 0 1 0 0 0 0 0 0 0 0 0 5.5151 -1.1655 1.0305 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9463 -1.0105 0.5300 C 0 0 1 0 0 0 0 0 0 0 0 0 6.9721 0.3089 -0.2529 C 0 0 2 0 0 0 0 0 0 0 0 0 8.1151 1.0184 0.3832 C 0 0 2 0 0 0 0 0 0 0 0 0 8.9045 1.8840 -0.5346 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9237 -0.1828 0.9027 C 0 0 2 0 0 0 0 0 0 0 0 0 7.8625 -0.8595 1.5616 O 0 0 0 0 0 0 0 0 0 0 0 0 9.9005 0.2055 1.9413 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2273 -0.5044 1.7715 C 0 0 0 0 0 0 0 0 0 0 0 0 11.5953 -0.3915 0.3440 C 0 0 0 0 0 0 0 0 0 0 0 0 12.8009 -0.0146 -0.0229 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5653 -0.7145 -0.6658 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3349 -1.0005 -0.0987 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6228 1.6804 1.2978 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1790 2.6205 -0.5687 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6385 -0.5539 -1.0383 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.5011 -1.7780 -1.1490 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.7662 -1.9608 -2.6495 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.5502 -0.9639 -3.1732 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6793 -1.7416 -0.4590 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8184 -2.8408 0.3955 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.8288 -3.6287 -0.1933 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.0367 -3.5230 0.4600 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.9522 -4.2403 1.8128 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.6692 -3.7892 2.4675 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.1769 -2.4948 1.7980 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0820 -2.0807 2.5543 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8749 -3.4472 3.8097 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.8755 -5.6036 1.5777 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5367 -0.0148 0.2189 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9429 1.3000 0.1980 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8638 2.1485 0.4818 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1656 3.4476 0.1660 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9937 4.2967 0.6751 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8402 4.1556 2.0369 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3952 3.9887 0.8569 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.5735 3.0373 0.7038 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0352 1.6661 1.1424 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.0437 0.7538 1.2875 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5997 3.4675 1.5090 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7348 5.2108 0.3194 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0839 -2.9459 -5.9144 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1064 -1.1923 -5.1322 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6602 -2.1907 -5.3602 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9681 -3.0665 -3.0314 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0393 -1.9401 -1.2716 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3482 -1.5406 -0.7411 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5269 -1.4446 -1.9841 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5851 -0.5453 -3.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1381 1.5556 -2.4672 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5684 0.5735 -2.8211 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7831 1.2022 1.3178 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2375 -0.1169 1.1182 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2830 1.3861 0.1733 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3941 -1.6666 0.6932 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2509 -0.8759 2.0130 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9796 -1.9885 1.0713 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5021 -1.6817 -0.6524 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2065 0.4762 1.3593 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0986 0.2179 -1.6900 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5581 2.8160 -0.1179 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3530 2.5902 -1.8959 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3443 1.2713 -2.0672 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6902 2.7500 -1.1553 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8018 -0.8021 -0.9378 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4062 -0.8539 2.0799 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1642 -2.2194 0.9516 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1471 -1.8739 -0.1234 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1440 0.1335 -1.3211 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8621 1.6034 1.2842 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7591 1.6364 -1.6213 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9679 1.9842 -0.2605 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4838 2.9293 -0.4432 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1275 1.2922 1.9280 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5535 -0.0155 2.9897 H 0 0 0 0 0 0 0 0 0 0 0 0 12.0013 -0.0884 2.4468 H 0 0 0 0 0 0 0 0 0 0 0 0 11.1115 -1.6064 1.9885 H 0 0 0 0 0 0 0 0 0 0 0 0 13.1279 0.0858 -1.0506 H 0 0 0 0 0 0 0 0 0 0 0 0 13.5896 0.2320 0.7120 H 0 0 0 0 0 0 0 0 0 0 0 0 10.5190 0.0085 -1.5030 H 0 0 0 0 0 0 0 0 0 0 0 0 10.9082 -1.6816 -1.1439 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0760 1.1237 2.1395 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1281 2.6582 1.0996 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5934 1.9457 1.6191 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4492 3.1630 -1.4891 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5893 3.0200 0.3557 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0596 2.7500 -0.4928 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0514 0.2250 -1.7569 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8668 -2.6623 -0.8847 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2956 -2.9245 -2.7497 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0939 -0.2374 -3.6241 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8820 -3.4504 0.2902 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.4272 -2.5048 0.5617 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.7634 -4.1401 -0.1430 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.8325 -3.9551 2.4298 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8427 -4.5177 2.3630 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9844 -1.7472 1.7751 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3806 -2.7638 2.4930 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5740 -4.0596 4.2050 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.5317 -5.8437 0.8805 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2686 1.5965 -0.8387 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2995 3.6367 -0.9180 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0432 4.0070 0.1962 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2163 5.3667 0.4643 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3828 4.7480 2.5814 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2103 4.1142 1.9377 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8362 3.0285 -0.3722 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5587 1.8719 2.1367 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7043 0.8213 0.5616 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3163 2.7893 1.5826 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7325 5.2900 0.2538 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 1 0 11 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 24 25 1 0 24 26 1 0 26 27 1 1 26 28 1 0 28 29 1 0 29 30 1 0 30 31 2 0 30 32 1 0 32 33 1 0 19 34 1 1 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 45 46 1 0 46 47 1 0 45 48 1 0 44 49 1 0 36 50 1 0 50 51 1 0 51 52 1 0 52 53 1 0 53 54 1 0 54 55 1 0 53 56 1 0 56 57 1 0 57 58 1 0 58 59 1 0 57 60 1 0 56 61 1 0 38 3 1 0 46 41 1 0 58 51 1 0 12 7 1 0 20 15 1 0 27 22 1 0 16 10 1 0 23 19 1 0 33 26 1 0 1 62 1 0 2 63 1 0 2 64 1 0 3 65 1 1 5 66 1 1 7 67 1 1 8 68 1 0 8 69 1 0 9 70 1 0 9 71 1 0 11 72 1 1 12 73 1 0 12 74 1 0 13 75 1 0 13 76 1 0 14 77 1 0 14 78 1 0 15 79 1 1 16 80 1 6 17 81 1 0 17 82 1 0 18 83 1 0 18 84 1 0 20 85 1 6 21 86 1 0 21 87 1 0 22 88 1 6 23 89 1 6 24 90 1 1 25 91 1 0 25 92 1 0 25 93 1 0 28 94 1 0 28 95 1 0 29 96 1 0 29 97 1 0 31 98 1 0 31 99 1 0 32100 1 0 32101 1 0 34102 1 0 34103 1 0 34104 1 0 35105 1 0 35106 1 0 35107 1 0 36108 1 6 37109 1 1 38110 1 1 39111 1 0 41112 1 1 43113 1 0 43114 1 0 44115 1 1 45116 1 1 46117 1 6 47118 1 0 48119 1 0 49120 1 0 51121 1 6 53122 1 6 54123 1 0 54124 1 0 55125 1 0 56126 1 1 57127 1 6 58128 1 1 59129 1 0 60130 1 0 61131 1 0 M END

Standard InCHIKey	OKXQHXAEZMQAFY-NPOQUHPBSA-N
Standard InCHI	InChI=1S/C44H70O17/c1-19-7-12-44(55-17-19)20(2)30-27(61-44)14-25-23-6-5-21-13-22(8-10-42(21,3)24(23)9-11-43(25,30)4)56-41-38(60-40-36(53)34(51)32(49)28(15-45)57-40)37(33(50)29(16-46)58-41)59-39-35(52)31(48)26(47)18-54-39/h20-41,45-53H,1,5-18H2,2-4H3/t20-,21+,22-,23+,24-,25-,26+,27-,28+,29+,30-,31-,32+,33-,34-,35+,36+,37-,38+,39-,40-,41+,42-,43-,44+/m0/s1
SMILES	OC[C@H]1O[C@@H](O[C@H]2CC[C@]3([C@@H](C2)CC[C@@H]2[C@@H]3CC[C@]3([C@H]2C[C@H]2[C@@H]3[C@H](C)[C@]3(O2)CCC(=C)CO3)C)C)[C@@H]([C@H]([C@H]1O)O[C@@H]1OC[C@H]([C@@H]([C@H]1O)O)O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	870.46	Volume:	839.369 ? Van der Waals volume.
Dense:	1.037	LogP:	1.571 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.402 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.191 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	49.0
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:	0.113	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.715	Fsp³:	0.955
MCE-18:	227.767 ? 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:	0.635	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.009 ? 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:	0.221	Promiscuous compounds:	0.05

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.123	MDCK Permeability:	-5.2
Pgp-inhibitor:	0.0	Pgp-substrate:	0.101
PAMPA:	0.964 ? 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%):	0.012	30% Bioavailability (F30%):	0.947
50% Bioavailability (F50%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.109	MRP1:	0.028
Plasma Protein Binding (PPB):	61.486%	Volume Distribution (VD):	-0.481
Fu:	33.075% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.027
BSEP inhibitor:	0.049

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.998	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.013
HLM stability:	0.0 ? 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):

0.34

Half-life (T1/2):

2.629

ADMET: Toxicity

hERG Blockers:	0.011	hERG Blockers (10um):	0.028
Human Hepatotoxicity (H-HT):	0.59	Drug-induced Liver Injury (DILI):	0.969
AMES Toxicity:	0.945	Rat Oral Acute Toxicity:	0.003
Maximum Recommended Daily Dose:	0.006	Skin Sensitization:	1.0
Carcinogencity:	0.078	Eye Corrosion:	0.0
Eye Irritation:	0.003	Respiratory Toxicity:	0.001
Drug-induced Neurotoxicity:	0.001	Ototoxicity:	0.998
Hematotoxicity:	0.37	Drug-induced Nephrotoxicity:	0.733
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.265
A549 Cytotoxicity:	0.851	Hek293 Cytotoxicity:	0.867
BCF:	1.633 ? 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:	3.393 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.546 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.961 ? 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
NPO1943	Yucca schidigera	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10757713]
NPO1943	Yucca schidigera	Species	Asparagaceae	Eukaryota	bark	n.a.	n.a.	PMID[15165156]
NPO1943	Yucca schidigera	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1943	Yucca schidigera	Species	Asparagaceae	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
MIC	6

Activity Type	# Activity
Organism	6

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
NPT312	Organism	Saccharomyces cerevisiae	Saccharomyces cerevisiae	MIC	=	12.5	ug.mL-1	PubChem BioAssay data set
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	12.5	ug.mL-1	DOI[10.6019/CHEMBL1201861]
NPT772	Organism	Pichia anomala	Wickerhamomyces anomalus	MIC	=	3.13	ug.mL-1	DOI[10.6019/CHEMBL1201861]
NPT5427	Organism	Hanseniaspora uvarum	Hanseniaspora uvarum	MIC	>	100.0	ug.mL-1	PMID[20041704]
NPT5425	Organism	Pichia nakazawae	Pichia nakazawae	MIC	=	3.13	ug.mL-1	PMID[14987066]
NPT5426	Organism	Debaryomyces hansenii	Debaryomyces hansenii	MIC	>	100.0	ug.mL-1	PMID[17190454]

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 NPC49032 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	25616
0.1-0.2	20932
0.2-0.3	2579
0.3-0.4	466
0.4-0.5	143
0.5-0.6	59
0.6-0.7	44
0.7-0.8	0
0.8-0.85	3
0.85-0.9	2
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC51172
0.9213	High Similarity	NPC125324
0.871	High Similarity	NPC475351
0.85	High Similarity	NPC108072
0.8454	Intermediate Similarity	NPC151134
0.8	Intermediate Similarity	NPC97700
0.8	Intermediate Similarity	NPC30856
0.7957	Intermediate Similarity	NPC206003
0.7957	Intermediate Similarity	NPC473610
0.7477	Intermediate Similarity	NPC132080
0.7429	Intermediate Similarity	NPC116756
0.7404	Intermediate Similarity	NPC475319
0.7327	Intermediate Similarity	NPC473601
0.7196	Intermediate Similarity	NPC232037
0.7048	Intermediate Similarity	NPC128572
0.6964	Remote Similarity	NPC470866
0.6916	Remote Similarity	NPC115165
0.6847	Remote Similarity	NPC233433
0.6822	Remote Similarity	NPC184617
0.6635	Remote Similarity	NPC160426
0.66	Remote Similarity	NPC250393
0.6518	Remote Similarity	NPC470864
0.6471	Remote Similarity	NPC211354
0.6471	Remote Similarity	NPC107188
0.6465	Remote Similarity	NPC297348
0.6465	Remote Similarity	NPC249204
0.6465	Remote Similarity	NPC48339
0.6465	Remote Similarity	NPC141769
0.6465	Remote Similarity	NPC477547
0.6441	Remote Similarity	NPC220836
0.6429	Remote Similarity	NPC232611
0.6379	Remote Similarity	NPC470867
0.6339	Remote Similarity	NPC475625
0.6339	Remote Similarity	NPC473518
0.633	Remote Similarity	NPC300557
0.6316	Remote Similarity	NPC476112
0.6316	Remote Similarity	NPC307534
0.6311	Remote Similarity	NPC54619
0.63	Remote Similarity	NPC325828
0.63	Remote Similarity	NPC177834
0.6286	Remote Similarity	NPC6295
0.6238	Remote Similarity	NPC234352
0.6216	Remote Similarity	NPC98018
0.6216	Remote Similarity	NPC284104
0.6216	Remote Similarity	NPC103616
0.6207	Remote Similarity	NPC31896
0.6202	Remote Similarity	NPC481189
0.6186	Remote Similarity	NPC94086
0.6186	Remote Similarity	NPC473817
0.6182	Remote Similarity	NPC471464
0.6176	Remote Similarity	NPC477451
0.6174	Remote Similarity	NPC83137
0.6147	Remote Similarity	NPC475643
0.6147	Remote Similarity	NPC602423
0.6095	Remote Similarity	NPC264101
0.6094	Remote Similarity	NPC329807
0.6053	Remote Similarity	NPC309278
0.6038	Remote Similarity	NPC107962
0.6	Remote Similarity	NPC19400
0.5909	Remote Similarity	NPC329727
0.5882	Remote Similarity	NPC481423
0.5859	Remote Similarity	NPC330026
0.5854	Remote Similarity	NPC210569
0.5847	Remote Similarity	NPC84111
0.5847	Remote Similarity	NPC287483
0.5847	Remote Similarity	NPC470865
0.5833	Remote Similarity	NPC262050
0.563	Remote Similarity	NPC470862
0.5614	Remote Similarity	NPC42171
0.5583	Remote Similarity	NPC477811
0.5524	Remote Similarity	NPC13190
0.5522	Remote Similarity	NPC329820
0.552	Remote Similarity	NPC477808
0.5508	Remote Similarity	NPC475333
0.5508	Remote Similarity	NPC224098
0.5508	Remote Similarity	NPC208383
0.5469	Remote Similarity	NPC263359
0.5455	Remote Similarity	NPC92297
0.544	Remote Similarity	NPC473505
0.5429	Remote Similarity	NPC481424
0.5429	Remote Similarity	NPC481422
0.5424	Remote Similarity	NPC470863
0.542	Remote Similarity	NPC481190
0.5417	Remote Similarity	NPC218571
0.5417	Remote Similarity	NPC487615
0.5366	Remote Similarity	NPC232054
0.536	Remote Similarity	NPC480556
0.5351	Remote Similarity	NPC202898
0.5349	Remote Similarity	NPC244431
0.5349	Remote Similarity	NPC305771
0.5349	Remote Similarity	NPC94072
0.5349	Remote Similarity	NPC169816
0.5339	Remote Similarity	NPC51520
0.5339	Remote Similarity	NPC303069
0.5333	Remote Similarity	NPC485594
0.5327	Remote Similarity	NPC294686
0.5315	Remote Similarity	NPC215408
0.5268	Remote Similarity	NPC485595
0.5263	Remote Similarity	NPC112274
0.5254	Remote Similarity	NPC294129
0.5221	Remote Similarity	NPC195297
0.5197	Remote Similarity	NPC477807
0.5169	Remote Similarity	NPC480555
0.5169	Remote Similarity	NPC150372
0.5156	Remote Similarity	NPC273002
0.514	Remote Similarity	NPC181845
0.514	Remote Similarity	NPC481425
0.514	Remote Similarity	NPC481426
0.5128	Remote Similarity	NPC92890
0.5116	Remote Similarity	NPC15918
0.5104	Remote Similarity	NPC481427
0.5091	Remote Similarity	NPC222731
0.5085	Remote Similarity	NPC274200
0.5046	Remote Similarity	NPC291203
0.5046	Remote Similarity	NPC217205
0.5043	Remote Similarity	NPC113044
0.5043	Remote Similarity	NPC283829
0.5043	Remote Similarity	NPC161676

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC49032 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7775
0.1-0.2	1296
0.2-0.3	62
0.3-0.4	11
0.4-0.5	4
0.5-0.6	1
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
0.63	Remote Similarity	NPD8171	Phase 2
0.5405	Remote Similarity	NPD8170	Phase 2

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