NPASS Compound

Natural Product: NPC50727

Natural Product ID	NPC50727
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	HTURSHLCTQHPMM-ZGXDEBHDSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	71581120
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 136143 0 0 0 0 0 0 0 0999 V2000 11.7364 3.2793 -0.3071 C 0 0 0 0 0 0 0 0 0 0 0 0 10.4284 2.3713 -0.5078 C 0 0 2 0 0 0 0 0 0 0 0 0 10.2476 1.6806 0.7731 C 0 0 0 0 0 0 0 0 0 0 0 0 9.2198 0.7915 1.2100 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8440 -0.5236 0.7123 C 0 0 2 0 0 0 0 0 0 0 0 0 8.3469 -0.7420 -0.6439 C 0 0 1 0 0 0 0 0 0 0 0 0 9.3679 -1.6091 -1.4220 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1309 -1.6596 -0.5062 C 0 0 1 0 0 0 0 0 0 0 0 0 7.2500 -2.1023 0.9312 C 0 0 2 0 0 0 0 0 0 0 0 0 5.8019 -2.2671 1.4210 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9632 -2.0019 0.2184 C 0 0 1 0 0 0 0 0 0 0 0 0 3.6097 -1.4153 0.5130 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7772 -2.5604 1.1168 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3926 -2.0515 1.2149 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9126 -1.0225 0.5363 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4964 -0.6306 0.7421 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2597 -0.9066 -0.5274 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3631 -0.8686 -1.7158 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8123 0.0479 -1.6148 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7125 -0.2103 -0.4363 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0298 1.0896 0.2795 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9360 -1.0147 -0.7572 C 0 0 1 0 0 0 0 0 0 0 0 0 3.7960 -0.3041 -1.7323 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1989 -0.8336 -1.8758 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8199 -0.9673 -0.5306 C 0 0 2 0 0 0 0 0 0 0 0 0 5.8239 0.3483 0.1805 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3977 -0.1107 -0.6225 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5850 -0.7932 -0.6334 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3282 -0.6218 0.7092 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.7530 0.8120 0.8817 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.4141 1.3650 -0.3614 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.8969 0.7910 -1.6288 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.9128 1.7438 -2.3260 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4556 3.0499 -2.2897 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4687 -0.5011 -1.6158 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8084 1.2509 -0.2523 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.4422 2.4851 -0.1384 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.3414 2.6744 -1.3165 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.7299 3.1296 -0.9064 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.6071 4.2447 0.1105 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.8032 3.7533 1.2641 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.7920 4.8003 1.7352 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1114 2.5920 1.0757 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.8927 4.5534 0.5397 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.4728 3.5254 -2.0152 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8244 3.6853 -2.1221 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6991 1.6293 1.2873 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3421 -1.5236 0.8587 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1994 -2.4565 1.8698 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.2843 -2.1716 2.8777 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.8972 -3.4498 3.3979 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.5192 -4.2490 2.2580 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.7113 -3.9950 0.9914 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.7387 -5.1227 0.0260 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3895 -3.6980 1.3178 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.7947 -3.7436 2.0438 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9467 -4.2715 3.9967 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7635 -1.5134 4.0196 O 0 0 0 0 0 0 0 0 0 0 0 0 7.8988 -1.1159 1.6105 O 0 0 0 0 0 0 0 0 0 0 0 0 9.9817 -1.4015 0.9216 O 0 0 0 0 0 0 0 0 0 0 0 0 10.8456 1.5778 -1.7119 C 0 0 0 0 0 0 0 0 0 0 0 0 11.1595 2.4933 -2.7749 O 0 0 0 0 0 0 0 0 0 0 0 0 12.4612 2.5693 0.1206 H 0 0 0 0 0 0 0 0 0 0 0 0 11.4710 4.1333 0.3055 H 0 0 0 0 0 0 0 0 0 0 0 0 12.0699 3.6105 -1.2940 H 0 0 0 0 0 0 0 0 0 0 0 0 9.6467 3.0954 -0.7004 H 0 0 0 0 0 0 0 0 0 0 0 0 11.2628 1.1253 1.0261 H 0 0 0 0 0 0 0 0 0 0 0 0 10.4016 2.5432 1.5646 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4565 0.5873 2.3555 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2222 1.3977 1.3614 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1193 0.1118 -1.2744 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3748 -1.2171 -1.1482 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2592 -2.6376 -1.0133 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1792 -1.5200 -2.4905 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1439 -2.5036 -1.1930 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7283 -3.0957 1.0225 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6336 -1.4952 2.1747 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6483 -3.2812 1.8653 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8848 -2.8786 -0.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6764 -0.6529 1.2932 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1919 -2.7964 2.1391 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8030 -3.4377 0.4722 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7413 -2.6028 1.9216 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5362 0.4705 0.9951 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8916 -1.1749 1.6091 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6347 -1.9703 -0.4550 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0194 -1.8728 -2.0020 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9514 -0.5273 -2.6027 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4887 1.1259 -1.5505 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3697 -0.0204 -2.5571 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4918 0.9645 1.2623 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0741 1.6561 0.4806 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6530 1.7546 -0.3269 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5668 -1.9638 -1.2309 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8220 0.8003 -1.6511 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3244 -0.4793 -2.7503 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2124 -1.7747 -2.4570 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7712 -0.0668 -2.4577 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0529 0.2820 1.2664 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5769 1.0035 -0.3362 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8765 0.8764 0.0821 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3247 -1.8911 -0.6257 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5667 -0.8424 1.4715 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5059 0.8400 1.6919 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2072 2.4555 -0.3625 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7837 0.8010 -2.3464 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9365 1.7812 -1.8458 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8741 1.4672 -3.3982 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9684 3.2370 -3.1410 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6594 3.2675 -0.1555 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4650 1.7770 -1.9406 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.2846 2.3109 -0.4102 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1353 5.1422 -0.3510 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.4876 3.6148 2.1445 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2670 5.6364 2.2496 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1601 4.2596 2.4992 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1024 5.0955 0.9216 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.0085 5.4840 0.8146 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.4300 3.5398 -1.7093 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4717 3.2980 -2.9605 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4049 2.1856 0.5208 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2493 -2.3565 2.4258 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0574 -1.4793 2.4782 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6863 -3.2211 4.1258 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5868 -5.3149 2.4431 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1208 -3.0830 0.5157 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7404 -5.5286 -0.2389 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4239 -5.9617 0.3494 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1933 -4.7679 -0.9361 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1354 -3.2002 2.8050 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6366 -4.9413 3.3476 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8083 -1.7188 4.1342 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1923 -1.2335 1.8805 H 0 0 0 0 0 0 0 0 0 0 0 0 10.0143 0.9668 -2.0687 H 0 0 0 0 0 0 0 0 0 0 0 0 11.7260 0.9732 -1.4805 H 0 0 0 0 0 0 0 0 0 0 0 0 11.4860 1.9334 -3.4955 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 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 1 20 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 1 17 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 32 33 1 0 33 34 1 0 32 35 1 0 31 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 39 40 1 0 40 41 1 0 41 42 1 0 41 43 1 0 40 44 1 0 39 45 1 0 38 46 1 0 30 47 1 0 29 48 1 0 48 49 1 0 49 50 1 0 50 51 1 0 51 52 1 0 52 53 1 0 53 54 1 0 53 55 1 0 52 56 1 0 51 57 1 0 50 58 1 0 9 59 1 0 5 60 1 6 2 61 1 0 61 62 1 0 59 5 1 0 25 8 1 0 35 28 1 0 43 37 1 0 55 49 1 0 25 11 1 0 22 12 1 0 20 15 1 0 1 63 1 0 1 64 1 0 1 65 1 0 2 66 1 6 3 67 1 0 3 68 1 0 4 69 1 0 4 70 1 0 6 71 1 6 7 72 1 0 7 73 1 0 7 74 1 0 8 75 1 6 9 76 1 6 10 77 1 0 10 78 1 0 11 79 1 6 12 80 1 1 13 81 1 0 13 82 1 0 14 83 1 0 16 84 1 0 16 85 1 0 17 86 1 1 18 87 1 0 18 88 1 0 19 89 1 0 19 90 1 0 21 91 1 0 21 92 1 0 21 93 1 0 22 94 1 6 23 95 1 0 23 96 1 0 24 97 1 0 24 98 1 0 26 99 1 0 26100 1 0 26101 1 0 28102 1 6 29103 1 1 30104 1 1 31105 1 6 32106 1 6 33107 1 0 33108 1 0 34109 1 0 37110 1 1 38111 1 6 39112 1 1 40113 1 6 41114 1 1 42115 1 0 42116 1 0 42117 1 0 44118 1 0 45119 1 0 46120 1 0 47121 1 0 49122 1 1 50123 1 6 51124 1 1 52125 1 1 53126 1 6 54127 1 0 54128 1 0 54129 1 0 56130 1 0 57131 1 0 58132 1 0 60133 1 0 61134 1 0 61135 1 0 62136 1 0 M END

Standard InCHIKey	HTURSHLCTQHPMM-ZGXDEBHDSA-N
Standard InCHI	InChI=1S/C45H74O17/c1-19(17-46)9-14-45(55)20(2)30-28(62-45)16-27-25-8-7-23-15-24(10-12-43(23,5)26(25)11-13-44(27,30)6)58-42-39(61-41-36(53)34(51)32(49)22(4)57-41)37(54)38(29(18-47)59-42)60-40-35(52)33(50)31(48)21(3)56-40/h7,19-22,24-42,46-55H,8-18H2,1-6H3/t19-,20+,21+,22+,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	C[C@H](CC[C@@]1([C@@H](C)[C@H]2[C@H](C[C@H]3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O)O)O)O)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O)O)O)O1)O)CO

Calculated Properties

Physi-Chem Properties

Molecular Weight:	886.49	Volume:	865.222 ? Van der Waals volume.
Dense:	1.025	LogP:	1.791 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.673 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.588 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	11.0	Rigid Bonds:	42.0
TPSA:	266.91 ? Topological Polar Surface Area.	H-Bond Acceptor:	17.0
H-Bond Donor:	10.0	Rings:	8.0
Heavy Atoms:	17.0

MedChem Properties

QED Drug-Likeness Score:	0.124	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.313	Fsp³:	0.956
MCE-18:	155.455 ? 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:	0.668	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:	0.27	Promiscuous compounds:	0.058

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.515	MDCK Permeability:	-5.006
Pgp-inhibitor:	0.0	Pgp-substrate:	0.967
PAMPA:	1.0 ? 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):	0.02
20% Bioavailability (F20%):	0.097	30% Bioavailability (F30%):	0.826
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.018
Plasma Protein Binding (PPB):	55.602%	Volume Distribution (VD):	-0.379
Fu:	32.215% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.07
BSEP inhibitor:	0.014

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:	0.975	CYP3A4-substrate:	0.998
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.592
HLM stability:	0.139 ? 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):

0.151

Half-life (T1/2):

3.414

ADMET: Toxicity

hERG Blockers:	0.025	hERG Blockers (10um):	0.172
Human Hepatotoxicity (H-HT):	0.296	Drug-induced Liver Injury (DILI):	0.416
AMES Toxicity:	0.529	Rat Oral Acute Toxicity:	0.003
Maximum Recommended Daily Dose:	0.006	Skin Sensitization:	1.0
Carcinogencity:	0.009	Eye Corrosion:	0.0
Eye Irritation:	0.001	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.998
Hematotoxicity:	0.086	Drug-induced Nephrotoxicity:	0.654
Genotoxicity:	0.002	RPMI-8226 Immunitoxicity:	0.216
A549 Cytotoxicity:	0.414	Hek293 Cytotoxicity:	0.454
BCF:	1.523 ? 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:	3.43 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.703 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.005 ? 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
NPO30749	Dioscorea panthalca	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]

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

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

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 NPC50727 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	24220
0.1-0.2	22421
0.2-0.3	2590
0.3-0.4	488
0.4-0.5	62
0.5-0.6	34
0.6-0.7	27
0.7-0.8	1
0.8-0.85	5
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8421	Intermediate Similarity	NPC73243
0.8421	Intermediate Similarity	NPC244086
0.8421	Intermediate Similarity	NPC84956
0.8247	Intermediate Similarity	NPC247037
0.8	Intermediate Similarity	NPC249265
0.7921	Intermediate Similarity	NPC23808
0.7921	Intermediate Similarity	NPC87998
0.7292	Intermediate Similarity	NPC94272
0.72	Intermediate Similarity	NPC122819
0.7172	Intermediate Similarity	NPC98696
0.71	Intermediate Similarity	NPC470433
0.71	Intermediate Similarity	NPC46190
0.71	Intermediate Similarity	NPC171073
0.703	Intermediate Similarity	NPC248746
0.699	Remote Similarity	NPC102016
0.699	Remote Similarity	NPC95051
0.6893	Remote Similarity	NPC480555
0.6893	Remote Similarity	NPC150372
0.6796	Remote Similarity	NPC42171
0.6774	Remote Similarity	NPC165439
0.6731	Remote Similarity	NPC475182
0.6698	Remote Similarity	NPC269297
0.6698	Remote Similarity	NPC222202
0.6667	Remote Similarity	NPC218571
0.6667	Remote Similarity	NPC487615
0.6667	Remote Similarity	NPC480554
0.6636	Remote Similarity	NPC475333
0.6636	Remote Similarity	NPC224098
0.6636	Remote Similarity	NPC208383
0.6574	Remote Similarity	NPC194207
0.6574	Remote Similarity	NPC22779
0.6545	Remote Similarity	NPC480553
0.6486	Remote Similarity	NPC287885
0.6286	Remote Similarity	NPC265275
0.6283	Remote Similarity	NPC232054
0.6261	Remote Similarity	NPC480556
0.6239	Remote Similarity	NPC486386
0.6195	Remote Similarity	NPC308140
0.6126	Remote Similarity	NPC254255
0.6068	Remote Similarity	NPC224314
0.6019	Remote Similarity	NPC124677
0.5962	Remote Similarity	NPC15249
0.5962	Remote Similarity	NPC25455
0.5849	Remote Similarity	NPC113044
0.5849	Remote Similarity	NPC283829
0.5849	Remote Similarity	NPC161676
0.581	Remote Similarity	NPC470432
0.581	Remote Similarity	NPC230507
0.5752	Remote Similarity	NPC32361
0.5752	Remote Similarity	NPC13193
0.5701	Remote Similarity	NPC305423
0.5688	Remote Similarity	NPC602423
0.5676	Remote Similarity	NPC150057
0.5676	Remote Similarity	NPC147753
0.5586	Remote Similarity	NPC300557
0.55	Remote Similarity	NPC486114
0.5446	Remote Similarity	NPC6806
0.5413	Remote Similarity	NPC14704
0.5377	Remote Similarity	NPC19400
0.5377	Remote Similarity	NPC476538
0.5377	Remote Similarity	NPC476539
0.5357	Remote Similarity	NPC477809
0.5345	Remote Similarity	NPC309278
0.5278	Remote Similarity	NPC485601
0.5242	Remote Similarity	NPC477808
0.5229	Remote Similarity	NPC485595
0.5229	Remote Similarity	NPC6295
0.5143	Remote Similarity	NPC291203
0.5143	Remote Similarity	NPC217205
0.5135	Remote Similarity	NPC470748
0.5135	Remote Similarity	NPC600116
0.5128	Remote Similarity	NPC475550
0.5096	Remote Similarity	NPC181845
0.5048	Remote Similarity	NPC485602
0.5044	Remote Similarity	NPC486388

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC50727 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7808
0.1-0.2	1279
0.2-0.3	53
0.3-0.4	8
0.4-0.5	0
0.5-0.6	1
0.6-0.7	0
0.7-0.8	1
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
0.72	Intermediate Similarity	NPD8449	Approved
0.5676	Remote Similarity	NPD8450	Suspended

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