NPASS Compound

Natural Product: NPC469420

Natural Product ID	NPC469420
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Paeonidanin D
IUPAC Name	n.a.
Synonyms	Paeonidanin D
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1078415
PubChem CID	46883514
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides

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

Chemical Representations

RDKit 2D 124133 0 0 0 0 0 0 0 0999 V2000 -3.0913 -8.3298 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8566 -6.8483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6220 -5.3668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8948 -4.0548 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6673 -2.7691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2669 -2.2315 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5323 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5323 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2669 2.2315 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5016 3.7131 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9020 4.2506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0677 3.3066 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1366 5.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9709 6.6761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2055 8.1577 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6059 8.6952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7716 7.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5370 6.2697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3943 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2760 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3943 -1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8578 -2.6401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0426 -0.3234 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0556 -0.1604 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7993 2.7796 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2158 2.5838 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6659 3.7974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5475 5.0109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1994 5.6685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0947 7.1648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5154 8.5351 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3663 9.7486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4270 8.6880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4876 9.7486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4270 10.8093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6405 11.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8540 12.5727 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2243 11.9626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3811 10.4708 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4379 12.8442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8082 12.2341 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0217 13.1158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8649 14.6076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4946 15.2177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2811 14.3360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7460 12.1458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7356 11.9112 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9702 10.4296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3067 9.7486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5310 11.4580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0028 11.1681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4045 11.7021 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1463 12.6834 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3810 14.1649 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3383 8.0036 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6865 7.3460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7911 5.8497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4012 4.4794 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1783 7.1892 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2200 9.2171 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1671 -2.7953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8943 -4.1072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1217 -5.3929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5221 -5.9305 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0600 -3.1632 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9324 -1.3137 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9256 -9.2738 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3751 -7.0829 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3557 -6.7960 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2037 -5.8551 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3013 -1.4097 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9877 -0.3870 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8952 -2.2054 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7143 1.6735 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0320 2.9816 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7660 2.1792 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4821 6.4934 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1636 9.2367 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8406 10.1767 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1720 8.2888 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7027 5.3257 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6933 1.9635 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3213 -4.0667 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2844 -2.1766 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5688 -3.1036 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4949 2.0107 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5599 0.5789 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8794 2.9157 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5477 4.6790 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5895 3.9319 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4053 7.1649 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7127 7.9155 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6545 7.4022 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9876 9.7486 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2524 13.1399 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6635 10.5940 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9650 10.7423 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3920 12.5057 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.0784 15.4893 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3378 16.7095 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9107 14.9461 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3577 13.5947 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7683 9.4113 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9877 11.0852 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1919 8.7450 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2385 12.7806 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5270 12.5213 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6156 15.6464 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8625 13.9302 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8995 14.3995 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5883 9.3027 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2726 8.7268 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2465 6.2126 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8930 4.3226 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0599 8.4028 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7117 9.0603 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5854 -2.3069 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0264 -5.0913 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0171 -6.8893 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7568 -7.4120 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4604 -3.7008 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0981 -0.3697 0.0000 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 7 6 1 1 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 6 11 12 1 0 12 13 1 0 13 14 2 0 13 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 10 21 1 0 21 22 1 0 22 23 1 0 23 24 1 1 23 25 1 0 25 26 1 0 26 27 2 0 21 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 32 33 1 0 34 33 1 6 34 35 1 0 35 36 1 0 36 37 1 0 37 38 1 1 38 39 1 0 39 40 1 0 40 41 2 0 40 42 1 0 42 43 2 0 43 44 1 0 44 45 2 0 45 46 1 0 46 47 2 0 37 48 1 0 48 49 1 0 49 50 1 0 50 51 1 6 50 52 1 0 52 53 1 0 53 54 2 0 48 55 1 0 55 56 1 0 32 57 1 0 57 58 1 0 58 59 1 0 59 60 1 0 58 61 1 0 57 62 1 0 5 63 1 0 63 64 1 0 64 65 1 0 65 66 1 0 64 67 1 0 63 68 1 0 65 3 1 0 23 7 1 0 59 30 1 0 10 7 1 0 20 15 1 0 50 34 1 0 26 9 1 0 37 34 1 0 47 42 1 0 53 36 1 0 1 69 1 0 2 70 1 0 2 71 1 0 3 72 1 1 5 73 1 1 8 74 1 0 8 75 1 0 9 76 1 6 11 77 1 0 11 78 1 0 16 79 1 0 17 80 1 0 18 81 1 0 19 82 1 0 20 83 1 0 21 84 1 6 24 85 1 0 24 86 1 0 24 87 1 0 25 88 1 0 25 89 1 0 29 90 1 0 29 91 1 0 30 92 1 6 32 93 1 6 35 94 1 0 35 95 1 0 36 96 1 6 38 97 1 0 38 98 1 0 43 99 1 0 44100 1 0 45101 1 0 46102 1 0 47103 1 0 48104 1 1 51105 1 0 51106 1 0 51107 1 0 52108 1 0 52109 1 0 56110 1 0 56111 1 0 56112 1 0 57113 1 1 58114 1 6 59115 1 1 60116 1 0 61117 1 0 62118 1 0 63119 1 6 64120 1 1 65121 1 6 66122 1 0 67123 1 0 68124 1 0 M END

Standard InCHIKey	QDMFASNVGVOIEZ-ASJHKIPBSA-N
Standard InCHI	InChI=1S/C47H56O21/c1-42-16-26(49)24-14-46(42,44(24,40(59-3)67-42)20-61-36(57)22-10-6-4-7-11-22)66-39-35(56)33(54)31(52)29(64-39)19-60-41-45(21-62-37(58)23-12-8-5-9-13-23)25-15-47(45,43(2,68-41)17-27(25)50)65-38-34(55)32(53)30(51)28(18-48)63-38/h4-13,24-25,28-35,38-41,48,51-56H,14-21H2,1-3H3/t24-,25-,28-,29-,30-,31-,32+,33+,34-,35-,38+,39+,40+,41+,42+,43+,44+,45+,46-,47-/m1/s1
SMILES	OC[C@H]1O[C@@H](O[C@]23C[C@H]4[C@@]3(COC(=O)c3ccccc3)[C@H](O[C@@]2(C)CC4=O)OC[C@H]2O[C@@H](O[C@]34C[C@H]5[C@@]4(COC(=O)c4ccccc4)[C@H](O[C@@]3(C)CC5=O)OC)[C@@H]([C@H]([C@@H]2O)O)O)[C@@H]([C@H]([C@@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	956.33	Volume:	894.133 ? Van der Waals volume.
Dense:	1.07	LogP:	1.042 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.558 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.944 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	17.0	Rigid Bonds:	50.0
TPSA:	302.19 ? Topological Polar Surface Area.	H-Bond Acceptor:	21.0
H-Bond Donor:	7.0	Rings:	12.0
Heavy Atoms:	21.0

MedChem Properties

QED Drug-Likeness Score:	0.102	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.872	Fsp³:	0.66
MCE-18:	245.846 ? 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:	0.957	Fluc inhibitor:	0.002 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.006 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.11 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.091	Promiscuous compounds:	0.244

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.939	MDCK Permeability:	-5.264
Pgp-inhibitor:	0.0	Pgp-substrate:	0.107
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):	0.003
20% Bioavailability (F20%):	0.0	30% Bioavailability (F30%):	0.059
50% Bioavailability (F50%):	0.218

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005	MRP1:	0.762
Plasma Protein Binding (PPB):	62.405%	Volume Distribution (VD):	-0.619
Fu:	57.758% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.014

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.038
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.459
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.977 ? 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):

0.718

Half-life (T1/2):

5.18

ADMET: Toxicity

hERG Blockers:	0.079	hERG Blockers (10um):	0.096
Human Hepatotoxicity (H-HT):	0.15	Drug-induced Liver Injury (DILI):	0.609
AMES Toxicity:	0.907	Rat Oral Acute Toxicity:	0.002
Maximum Recommended Daily Dose:	0.023	Skin Sensitization:	0.996
Carcinogencity:	0.113	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.048	Ototoxicity:	0.994
Hematotoxicity:	0.059	Drug-induced Nephrotoxicity:	0.665
Genotoxicity:	0.025	RPMI-8226 Immunitoxicity:	0.297
A549 Cytotoxicity:	0.506	Hek293 Cytotoxicity:	0.707
BCF:	0.419 ? 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:	3.383 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.463 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.312 ? 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
NPO30226	Paeonia albiflora	Species	Paeoniaceae	Eukaryota	roots	n.a.	n.a.	PMID[19691309]
NPO30226	Paeonia albiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO30226	Paeonia albiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30226	Paeonia albiflora	Species	Paeoniaceae	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

Activity Type	# Activity
Inhibition	4

Activity Type	# Activity
Cell line	4

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
NPT848	Cell line	N9	Homo sapiens	Inhibition	=	111.5	%	DOI[10.1016/S0960-894X(00)80319-4]
NPT848	Cell line	N9	Homo sapiens	Inhibition	=	96.6	%	PMID[19702283]
NPT848	Cell line	N9	Homo sapiens	Inhibition	=	83.5	%	PMID[11430012]
NPT848	Cell line	N9	Homo sapiens	Inhibition	=	77.1	%	PMID[19880317]

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 NPC469420 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	11626
0.1-0.2	32741
0.2-0.3	5015
0.3-0.4	421
0.4-0.5	16
0.5-0.6	27
0.6-0.7	8
0.7-0.8	0
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8571	High Similarity	NPC469417
0.8295	Intermediate Similarity	NPC469421
0.7952	Intermediate Similarity	NPC469419
0.7674	Intermediate Similarity	NPC469418
0.6778	Remote Similarity	NPC469398
0.6512	Remote Similarity	NPC469448
0.6364	Remote Similarity	NPC222102
0.6136	Remote Similarity	NPC303429
0.6136	Remote Similarity	NPC56594
0.6111	Remote Similarity	NPC469422
0.6	Remote Similarity	NPC34066
0.6	Remote Similarity	NPC190862
0.5909	Remote Similarity	NPC133430
0.5889	Remote Similarity	NPC469477
0.5778	Remote Similarity	NPC469399
0.5729	Remote Similarity	NPC469396
0.5729	Remote Similarity	NPC469458
0.5729	Remote Similarity	NPC149002
0.5684	Remote Similarity	NPC469415
0.5682	Remote Similarity	NPC478832
0.5638	Remote Similarity	NPC117943
0.5588	Remote Similarity	NPC188217
0.5568	Remote Similarity	NPC478830
0.5556	Remote Similarity	NPC260300
0.5495	Remote Similarity	NPC469456
0.549	Remote Similarity	NPC478828
0.5455	Remote Similarity	NPC80360
0.5426	Remote Similarity	NPC293568
0.5426	Remote Similarity	NPC161626
0.5393	Remote Similarity	NPC478831
0.5368	Remote Similarity	NPC120012
0.5333	Remote Similarity	NPC477617
0.5312	Remote Similarity	NPC88176
0.5283	Remote Similarity	NPC478826
0.5283	Remote Similarity	NPC478827
0.5189	Remote Similarity	NPC478829
0.5185	Remote Similarity	NPC469397
0.5149	Remote Similarity	NPC265600
0.5049	Remote Similarity	NPC148185

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC469420 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3747
0.1-0.2	5250
0.2-0.3	151
0.3-0.4	2
0.4-0.5	0
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