NPASS Compound

Natural Product: NPC208477

Natural Product ID	NPC208477
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Ginsenoside Rd
IUPAC Name	(2S,3R,4S,5S,6R)-2-[(2R,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[[(3S,5R,8R,9R,10R,12R,13R,14R,17S)-12-hydroxy-4,4,8,10,14-pentamethyl-17-[(2S)-6-methyl-2-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyhept-5-en-2-yl]-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]oxy]oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms	Ginsenoside Rd
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL473659
PubChem CID	11679800
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene 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 148154 0 0 0 0 0 0 0 0999 V2000 5.9793 -4.2988 -2.8953 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7960 -2.9350 -2.8909 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5702 -2.2414 -1.7747 C 0 0 1 0 0 0 0 0 0 0 0 0 6.3147 -0.9008 -1.8705 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8734 -0.3040 -0.6913 C 0 0 1 0 0 0 0 0 0 0 0 0 4.5659 -0.5712 -0.4049 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7416 0.5418 -0.4130 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8752 0.4279 -1.6453 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7033 -0.4628 -1.5193 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8583 -0.3237 -0.2783 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4653 0.7548 0.5343 C 0 0 2 0 0 0 0 0 0 0 0 0 2.9405 0.6173 0.8403 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2745 -0.4410 1.8196 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3066 1.9511 1.5108 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6620 1.2691 1.6622 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6715 1.7981 1.1029 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3795 0.7099 0.3540 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5107 0.1648 -0.7180 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2745 -0.8112 -1.5566 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3664 0.0242 -2.2537 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8098 -0.5230 -3.4035 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3513 0.3059 -1.1676 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6033 1.3115 -0.2882 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3169 2.5847 -1.0181 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7346 1.5697 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7982 1.9621 -0.3920 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6264 0.9463 -1.5370 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.8359 0.0254 -1.4888 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9935 -0.3684 -0.2078 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9942 -1.1947 0.1538 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.7435 -0.5907 1.1630 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6625 -1.4547 1.7431 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.7011 -0.6183 2.4558 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1194 0.1705 3.4426 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.9253 -2.2479 2.8067 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.5007 -2.4025 2.3110 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.4802 -2.5021 0.7833 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.3014 -3.5814 0.4608 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6652 -1.4213 2.7846 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5420 -3.4647 3.0186 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9634 0.4978 -2.2990 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6808 1.7504 -2.1093 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4010 1.9273 -0.8289 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3372 2.9587 -0.0236 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5018 4.1346 -0.3039 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1305 3.0042 1.2610 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4624 -1.3058 -2.2337 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8278 -0.2895 1.3790 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7886 -1.6801 0.3494 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7381 -0.6495 0.4848 C 0 0 1 0 0 0 0 0 0 0 0 0 6.6563 -2.1364 0.7250 C 0 0 2 0 0 0 0 0 0 0 0 0 6.1266 -2.8507 -0.4742 C 0 0 2 0 0 0 0 0 0 0 0 0 6.5213 -4.1877 -0.4891 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8628 -2.4282 1.8551 O 0 0 0 0 0 0 0 0 0 0 0 0 8.0864 -0.3593 0.2433 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5998 0.5589 1.1406 C 0 0 2 0 0 0 0 0 0 0 0 0 9.0712 1.6491 0.4297 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3163 1.4621 -0.1169 C 0 0 2 0 0 0 0 0 0 0 0 0 10.4657 2.3247 -1.3640 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3162 3.6686 -1.0588 O 0 0 0 0 0 0 0 0 0 0 0 0 10.6428 0.0265 -0.4014 C 0 0 2 0 0 0 0 0 0 0 0 0 10.6764 -0.7073 0.9182 C 0 0 1 0 0 0 0 0 0 0 0 0 9.6940 -0.1553 1.9210 C 0 0 1 0 0 0 0 0 0 0 0 0 10.2850 0.6594 2.8696 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3526 -2.0435 0.6942 O 0 0 0 0 0 0 0 0 0 0 0 0 11.9351 0.0035 -0.9732 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0878 -4.6378 -3.8048 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7044 -2.6949 -2.7914 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1004 -2.5428 -3.8881 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6442 -2.4998 -1.9629 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9421 0.8171 -0.8364 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3981 1.4227 -0.6043 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4817 0.0725 -2.5037 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5109 1.4363 -1.9386 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0275 -0.4028 -2.4222 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1260 -1.5119 -1.6136 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4738 1.6409 -0.1948 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5748 -0.5192 2.6751 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3999 -1.3972 1.2725 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2603 -0.2524 2.3107 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8340 2.7985 1.0110 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1263 1.8984 2.6009 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4208 2.0503 1.3993 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5083 0.6249 2.5123 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1781 2.1979 2.0443 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2908 2.0477 2.0052 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5175 2.7293 0.5680 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2668 1.0272 -1.4092 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7445 -1.3280 -2.3365 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8374 -1.5588 -0.9572 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8461 0.9907 -2.5297 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0956 0.1854 -4.0367 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5358 -0.5574 -0.4968 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2877 2.7638 -1.3120 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9433 2.7270 -1.9198 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5839 3.4364 -0.3274 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5860 2.3871 1.3530 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1490 0.6328 1.1164 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7444 1.8494 0.1266 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5393 2.9748 -0.6831 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5603 1.4203 -2.5215 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6976 -1.5245 -0.6261 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1781 -2.1037 1.0099 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.4154 -1.3036 2.9790 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.2816 0.0087 1.7736 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.5399 1.0614 3.5232 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9104 -1.6889 3.7587 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1358 -3.3867 2.6691 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4257 -2.6591 0.4952 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5431 -3.6082 -0.4795 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1362 -0.6036 3.0861 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3735 -3.3048 3.5302 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7390 -0.3280 -2.4603 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5378 0.5414 -3.3794 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5189 1.8217 -2.8915 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1040 2.6744 -2.3133 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.0853 1.1205 -0.4793 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6629 4.0119 -0.9783 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0454 4.4931 0.6695 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1577 4.9686 -0.6976 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.5186 4.0470 1.3421 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5067 2.7144 2.1304 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.9998 2.3177 1.1909 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6046 -1.7893 -1.8101 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3449 -1.9561 -2.0586 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4465 -1.1374 -3.3225 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4357 0.2951 2.1338 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3307 -1.1748 1.0036 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9815 -0.6684 2.0206 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4200 -2.4519 -0.1853 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2549 -2.0690 0.2131 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0350 -1.7652 1.3936 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3982 -0.0506 1.3622 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6637 -2.5245 0.9948 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0181 -2.8594 -0.4467 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5048 -4.2010 -0.6689 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2999 -3.2194 1.6426 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8139 0.8677 1.8709 H 0 0 0 0 0 0 0 0 0 0 0 0 11.0883 1.8290 0.6068 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7174 2.0431 -2.1364 H 0 0 0 0 0 0 0 0 0 0 0 0 11.4744 2.1929 -1.8122 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5120 3.7631 -0.4886 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9773 -0.4405 -1.1355 H 0 0 0 0 0 0 0 0 0 0 0 0 11.7150 -0.6990 1.3259 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1752 -0.9915 2.4590 H 0 0 0 0 0 0 0 0 0 0 0 0 11.2652 0.6439 2.7531 H 0 0 0 0 0 0 0 0 0 0 0 0 10.8714 -2.6279 1.2951 H 0 0 0 0 0 0 0 0 0 0 0 0 11.8420 0.1848 -1.9601 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 12 13 1 0 12 14 1 0 11 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 20 22 1 0 22 23 1 0 23 24 1 6 23 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 1 29 30 1 0 30 31 1 0 31 32 1 0 32 33 1 0 33 34 1 0 32 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 36 39 1 0 35 40 1 0 28 41 1 0 41 42 1 0 42 43 1 0 43 44 2 3 44 45 1 0 44 46 1 0 28 47 1 0 17 48 1 1 10 49 1 1 5 50 1 0 50 51 1 0 51 52 1 0 52 53 1 0 51 54 1 0 50 55 1 0 55 56 1 0 56 57 1 0 57 58 1 0 58 59 1 0 59 60 1 0 58 61 1 0 61 62 1 0 62 63 1 0 63 64 1 0 62 65 1 0 61 66 1 0 52 3 1 0 63 56 1 0 12 7 1 0 23 17 1 0 37 30 1 0 18 10 1 0 27 22 1 0 1 67 1 0 2 68 1 0 2 69 1 0 3 70 1 6 5 71 1 6 7 72 1 6 8 73 1 0 8 74 1 0 9 75 1 0 9 76 1 0 11 77 1 6 13 78 1 0 13 79 1 0 13 80 1 0 14 81 1 0 14 82 1 0 14 83 1 0 15 84 1 0 15 85 1 0 16 86 1 0 16 87 1 0 18 88 1 6 19 89 1 0 19 90 1 0 20 91 1 6 21 92 1 0 22 93 1 1 24 94 1 0 24 95 1 0 24 96 1 0 25 97 1 0 25 98 1 0 26 99 1 0 26100 1 0 27101 1 6 30102 1 6 32103 1 6 33104 1 0 33105 1 0 34106 1 0 35107 1 1 36108 1 1 37109 1 6 38110 1 0 39111 1 0 40112 1 0 41113 1 0 41114 1 0 42115 1 0 42116 1 0 43117 1 0 45118 1 0 45119 1 0 45120 1 0 46121 1 0 46122 1 0 46123 1 0 47124 1 0 47125 1 0 47126 1 0 48127 1 0 48128 1 0 48129 1 0 49130 1 0 49131 1 0 49132 1 0 50133 1 1 51134 1 1 52135 1 1 53136 1 0 54137 1 0 56138 1 1 58139 1 1 59140 1 0 59141 1 0 60142 1 0 61143 1 6 62144 1 1 63145 1 1 64146 1 0 65147 1 0 66148 1 0 M END

Standard InCHIKey	RLDVZILFNVRJTL-IWFVLDDISA-N
Standard InCHI	InChI=1S/C48H82O18/c1-22(2)10-9-14-48(8,66-42-39(60)36(57)33(54)26(20-50)62-42)23-11-16-47(7)31(23)24(52)18-29-45(5)15-13-30(44(3,4)28(45)12-17-46(29,47)6)64-43-40(37(58)34(55)27(21-51)63-43)65-41-38(59)35(56)32(53)25(19-49)61-41/h10,23-43,49-60H,9,11-21H2,1-8H3/t23-,24+,25+,26+,27+,28-,29+,30-,31-,32+,33+,34+,35-,36-,37-,38+,39+,40+,41-,42-,43-,45-,46+,47+,48-/m0/s1
SMILES	OC[C@H]1O[C@@H](O[C@H]2CC[C@]3([C@H](C2(C)C)CC[C@@]2([C@@H]3C[C@@H](O)[C@H]3[C@@]2(C)CC[C@@H]3[C@@](O[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O)O)O)(CCC=C(C)C)C)C)C)[C@@H]([C@H]([C@@H]1O)O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	946.55	Volume:	934.456 ? Van der Waals volume.
Dense:	1.013	LogP:	2.143 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.817 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.566 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	13.0	Rigid Bonds:	39.0
TPSA:	298.14 ? Topological Polar Surface Area.	H-Bond Acceptor:	18.0
H-Bond Donor:	12.0	Rings:	7.0
Heavy Atoms:	18.0

MedChem Properties

QED Drug-Likeness Score:	0.085	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.377	Fsp³:	0.958
MCE-18:	155.489 ? 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:	0.814	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.003 ? 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:	0.297	Promiscuous compounds:	0.201

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.576	MDCK Permeability:	-4.999
Pgp-inhibitor:	0.0	Pgp-substrate:	0.263
PAMPA:	0.999 ? 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):	0.819
20% Bioavailability (F20%):	0.121	30% Bioavailability (F30%):	0.997
50% Bioavailability (F50%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.033	MRP1:	0.114
Plasma Protein Binding (PPB):	67.412%	Volume Distribution (VD):	-0.421
Fu:	22.018% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.051	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.008	CYP3A4-substrate:	0.001
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.786
HLM stability:	0.033 ? 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):

0.122

Half-life (T1/2):

3.087

ADMET: Toxicity

hERG Blockers:	0.003	hERG Blockers (10um):	0.005
Human Hepatotoxicity (H-HT):	0.762	Drug-induced Liver Injury (DILI):	0.786
AMES Toxicity:	0.969	Rat Oral Acute Toxicity:	0.001
Maximum Recommended Daily Dose:	0.0	Skin Sensitization:	1.0
Carcinogencity:	0.072	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.001
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.792	Drug-induced Nephrotoxicity:	0.994
Genotoxicity:	0.091	RPMI-8226 Immunitoxicity:	0.199
A549 Cytotoxicity:	0.929	Hek293 Cytotoxicity:	0.34
BCF:	1.381 ? 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:	3.481 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.767 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.007 ? 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
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[ 12877918]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jarmap.2018.11.004]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jarmap.2018.11.004]
NPO25128	Panax vietnamensis	Species	Araliaceae	Eukaryota	n.a.	Vietnamese	n.a.	PMID[11325227]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12350149]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Flower buds	n.a.	n.a.	PMID[12880307]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Stems	n.a.	n.a.	PMID[17663584]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[18186611]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[18409045]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[19926279]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	Stems	n.a.	n.a.	PMID[20104880]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	root	n.a.	PMID[2092947]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	berry	n.a.	n.a.	PMID[21216145]
NPO28005.2	Panax japonicus var. major (burk.) wu et feng	Varieties	Araliaceae	Eukaryota	n.a.	root	n.a.	PMID[21417387]
NPO28005.2	Panax japonicus var. major (burk.) wu et feng	Varieties	Araliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[21417387]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22342101]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	leaves	n.a.	n.a.	PMID[24290061]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24968750]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25152999]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	leaves and stems	n.a.	n.a.	PMID[25442304]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	aerial parts	n.a.	n.a.	PMID[25895106]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Steamed Roots	n.a.	n.a.	PMID[26200131]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	stems-leaves	n.a.	n.a.	PMID[26420067]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	stem	n.a.	PMID[27914541]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28006911]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28202328]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	Flower Buds	n.a.	n.a.	PMID[28345906]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32129622]
NPO4305	Pertusaria wulfenii	Species	Pertusariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16506	Synotis alata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11990	Coleostephus myconis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO918	Dahlia pinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29812	Panax quinquefolium	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25128	Panax vietnamensis	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29812	Panax quinquefolium	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28005.2	Panax japonicus var. major (burk.) wu et feng	Varieties	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11990	Coleostephus myconis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO918	Dahlia pinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO918	Dahlia pinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11990	Coleostephus myconis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29812	Panax quinquefolium	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28005.2	Panax japonicus var. major (burk.) wu et feng	Varieties	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11990	Coleostephus myconis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO918	Dahlia pinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4305	Pertusaria wulfenii	Species	Pertusariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11990	Coleostephus myconis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25128	Panax vietnamensis	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16506	Synotis alata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	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	2
Inhibition	13
Activity	5
EC50	1
Survival	3

Activity Type	# Activity
Individual protein	4
Cell line	11
Organism	5
Single protein	1
Others	2
Protein complex	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1044	Individual protein	DNA topoisomerase II alpha	Homo sapiens	IC50	>	250000.0	nM	PMID[20371180]
NPT143	Individual protein	DNA topoisomerase I	Homo sapiens	IC50	>	250000.0	nM	PMID[20371180]
NPT20556	Single protein	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	7.699	%	DOI[10.6019/CHEMBL4495564]
NPT692	Individual protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	6.33	%	HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators
NPT692	Individual protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	0.27	%	HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT993	Cell line	Hepatocyte	Mus musculus	Inhibition	=	17.5	%	PMID[11325227]
NPT993	Cell line	Hepatocyte	Mus musculus	Inhibition	=	39.1	%	PMID[11325227]
NPT993	Cell line	Hepatocyte	Mus musculus	Inhibition	=	19.5	%	PMID[11325227]
NPT993	Cell line	Hepatocyte	Mus musculus	Activity	=	7.4	%	PMID[11325227]
NPT993	Cell line	Hepatocyte	Mus musculus	Activity	=	16.8	%	PMID[11325227]
NPT993	Cell line	Hepatocyte	Mus musculus	Activity	=	8.4	%	PMID[11325227]
NPT380	Cell line	U-251	Homo sapiens	Activity	=	78.36	%	PMID[25442304]
NPT76	Cell line	C6	Rattus norvegicus	Activity	=	102.07	%	PMID[25442304]
NPT20555	Organism	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-4.52	%	DOI[10.21203/rs.3.rs-23951/v1]
NPT20555	Organism	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-0.06	%	DOI[10.6019/CHEMBL4495565]
NPT23107	Protein complex	AMPK alpha2/beta1/gamma1	Homo sapiens	EC50	=	16.8	nM	PMID[28345906]
NPT2	Others	Unspecified	n.a.	Inhibition	=	-3.54	%	PMID[21417387]
NPT2	Others	Unspecified	n.a.	Inhibition	=	2.88	%	PMID[21417387]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT993	Cell line	Hepatocyte	Mus musculus	Survival	=	35.3	%	PMID[11325227]
NPT993	Cell line	Hepatocyte	Mus musculus	Survival	=	41.8	%	PMID[11325227]
NPT993	Cell line	Hepatocyte	Mus musculus	Survival	=	35.9	%	PMID[11325227]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	97.0	%	PMID[12880307]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	93.0	%	PMID[12880307]

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 NPC208477 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	22881
0.1-0.2	22507
0.2-0.3	3274
0.3-0.4	924
0.4-0.5	201
0.5-0.6	22
0.6-0.7	24
0.7-0.8	0
0.8-0.85	4
0.85-0.9	4
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9024	High Similarity	NPC208650
0.881	High Similarity	NPC220427
0.8667	High Similarity	NPC31907
0.8506	High Similarity	NPC14946
0.8506	High Similarity	NPC63368
0.8415	Intermediate Similarity	NPC269627
0.8395	Intermediate Similarity	NPC181467
0.8295	Intermediate Similarity	NPC159005
0.8222	Intermediate Similarity	NPC135369
0.7952	Intermediate Similarity	NPC69737
0.7872	Intermediate Similarity	NPC241381
0.7708	Intermediate Similarity	NPC488292
0.7708	Intermediate Similarity	NPC146868
0.7449	Intermediate Similarity	NPC488294
0.7381	Intermediate Similarity	NPC312553
0.7381	Intermediate Similarity	NPC8039
0.7381	Intermediate Similarity	NPC120123
0.7234	Intermediate Similarity	NPC246124
0.7229	Intermediate Similarity	NPC157659
0.7184	Intermediate Similarity	NPC488291
0.7143	Intermediate Similarity	NPC159036
0.7125	Intermediate Similarity	NPC66654
0.7079	Intermediate Similarity	NPC127801
0.6989	Remote Similarity	NPC65167
0.6774	Remote Similarity	NPC208594
0.6759	Remote Similarity	NPC488293
0.6705	Remote Similarity	NPC472987
0.6667	Remote Similarity	NPC472897
0.6667	Remote Similarity	NPC472896
0.6526	Remote Similarity	NPC472988
0.6526	Remote Similarity	NPC38217
0.6392	Remote Similarity	NPC160816
0.6344	Remote Similarity	NPC194842
0.6344	Remote Similarity	NPC472715
0.6316	Remote Similarity	NPC234160
0.625	Remote Similarity	NPC114874
0.6235	Remote Similarity	NPC234287
0.6235	Remote Similarity	NPC88000
0.6235	Remote Similarity	NPC4831
0.6235	Remote Similarity	NPC472023
0.6207	Remote Similarity	NPC160734
0.6154	Remote Similarity	NPC16573
0.6154	Remote Similarity	NPC165033
0.6154	Remote Similarity	NPC273879
0.6078	Remote Similarity	NPC180183
0.6	Remote Similarity	NPC280825
0.6	Remote Similarity	NPC473198
0.598	Remote Similarity	NPC472718
0.5922	Remote Similarity	NPC6931
0.5851	Remote Similarity	NPC139271
0.5833	Remote Similarity	NPC152584
0.5824	Remote Similarity	NPC611039
0.5761	Remote Similarity	NPC252253
0.5714	Remote Similarity	NPC472716
0.5699	Remote Similarity	NPC45959
0.5604	Remote Similarity	NPC309425
0.5596	Remote Similarity	NPC146652
0.551	Remote Similarity	NPC276758
0.5464	Remote Similarity	NPC213190
0.5417	Remote Similarity	NPC229801
0.5354	Remote Similarity	NPC304011
0.5243	Remote Similarity	NPC476360
0.5243	Remote Similarity	NPC476361
0.52	Remote Similarity	NPC236753
0.5152	Remote Similarity	NPC472252
0.5152	Remote Similarity	NPC245280
0.5152	Remote Similarity	NPC488574
0.5149	Remote Similarity	NPC164194
0.51	Remote Similarity	NPC307167

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC208477 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7720
0.1-0.2	1371
0.2-0.3	54
0.3-0.4	4
0.4-0.5	1
0.5-0.6	0
0.6-0.7	0
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
		NPD

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