NPASS Compound

Natural Product: NPC324460

Natural Product ID	NPC324460
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	JXLYSJRDGCGARV-PHYWHDLESA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	5315216
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 117125 0 0 0 0 0 0 0 0999 V2000 -5.7265 4.8953 0.3439 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8593 3.6430 1.1612 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6772 2.4182 0.2906 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3290 2.3865 -0.3681 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2896 1.1436 -1.2890 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9145 0.6475 -1.4724 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3990 -0.7625 -1.5503 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5598 -1.6682 -0.3867 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6319 -2.1762 0.2908 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0868 -2.1750 0.0568 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0481 -1.2561 0.6648 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0764 0.1034 0.1697 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.8247 0.0945 -0.4535 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9785 1.1630 1.1385 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1077 -3.0189 1.3057 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6994 -3.7879 2.3212 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9512 -4.5265 3.2090 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5723 -4.5227 3.1128 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9663 -3.7784 2.1282 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7564 -3.0425 1.2468 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4900 -2.2354 0.2300 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.9455 -0.2320 -1.5899 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4475 0.3731 -2.7279 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7066 1.0978 -2.7930 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4705 1.2603 -1.6339 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0169 0.6846 -0.4975 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1745 -0.0488 -0.4736 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0151 1.0119 0.5716 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2713 2.0470 1.4402 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8507 1.7294 2.8023 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8172 0.3044 2.7867 N 0 0 0 0 0 0 0 0 0 0 0 0 2.2600 -0.1335 1.4855 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5861 -0.7818 1.4502 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4269 -0.5757 2.6619 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9040 -0.3609 3.8403 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4089 -0.3345 3.9002 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4218 -0.4615 0.2471 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4422 0.9557 -0.1841 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1346 1.6779 -0.0772 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6976 1.9657 -1.4191 N 0 0 0 0 0 0 0 0 0 0 0 0 3.3366 2.8117 -2.4331 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4685 1.7537 0.5411 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3882 2.0154 1.7792 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5894 2.2673 -0.0963 O 0 0 0 0 0 0 0 0 0 0 0 0 7.5692 3.0329 0.6103 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8874 0.9043 -1.5332 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7706 -0.8130 0.5834 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4840 -1.7900 -0.0675 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9092 -2.4040 -1.0110 O 0 0 0 0 0 0 0 0 0 0 0 0 7.8882 -2.1476 0.2913 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4255 -2.3190 1.3823 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6792 -2.7540 0.1678 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2467 0.1819 -3.8774 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8256 0.7661 -5.1166 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5332 -1.4163 -2.8617 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4699 -1.1072 -3.6794 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6557 -2.3998 -3.2838 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8267 -3.0090 -4.5715 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6389 2.4925 -0.7156 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1048 4.7754 -0.6935 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3679 5.6957 0.8086 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6700 5.2163 0.3727 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0686 3.6502 1.9409 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8755 3.6053 1.5834 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2483 3.2856 -0.9798 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5028 2.2624 0.3580 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8324 1.3644 -2.2322 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5130 1.2308 -2.3394 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3261 1.0988 -0.5983 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3189 -2.4211 -1.0544 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5084 -3.1932 0.4042 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7967 -1.1663 1.7474 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0846 -1.6387 0.5740 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8911 -0.6947 -1.1732 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1236 0.0587 0.4043 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1217 1.0219 1.8305 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9180 1.3711 1.6550 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7733 -3.8060 2.4189 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4474 -5.0957 3.9647 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0012 -5.1121 3.8237 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0962 -3.7515 2.0249 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4390 -2.1977 -0.0843 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0001 1.5224 -3.7193 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4957 -0.3649 0.5381 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2079 1.8175 1.4657 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5153 3.0725 1.1002 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2100 2.1085 3.6241 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8580 2.1749 2.8350 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4925 -0.9226 1.2025 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5010 -0.6116 2.5458 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4935 -0.2125 4.7127 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1444 0.2442 4.8095 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9884 -1.3589 4.0687 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1497 -1.1408 -0.6051 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3002 2.7045 0.3821 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5439 3.4963 -2.8032 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7192 2.1900 -3.2668 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1059 3.4105 -1.9451 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3183 3.3370 -0.1505 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0162 2.4498 1.4419 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1075 3.9880 0.9842 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8627 1.0581 -1.5898 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5375 -1.6291 -0.4610 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0887 -3.2179 0.2544 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1318 -1.7324 1.3087 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4711 -2.7043 1.3119 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0060 -2.7069 2.3240 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2479 -1.9341 -0.4303 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3486 -3.3095 -0.5549 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8447 -3.4461 0.4202 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9113 1.8694 -5.0904 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4296 0.3970 -5.9462 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2529 0.5091 -5.3220 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4802 -2.2641 -5.3353 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9134 -3.1211 -4.7429 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2606 -3.9455 -4.6386 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2536 2.9231 -1.5320 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 2 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 12 14 1 0 9 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 20 21 1 0 7 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 25 26 1 0 26 27 2 0 26 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 34 35 2 0 35 36 1 0 33 37 1 0 37 38 1 0 38 39 1 0 39 40 1 0 40 41 1 0 38 42 1 0 42 43 2 0 42 44 1 0 44 45 1 0 38 46 1 0 37 47 1 0 47 48 1 0 48 49 2 0 48 50 1 0 33 51 1 0 51 52 1 0 23 53 1 0 53 54 1 0 7 55 1 0 55 56 2 0 55 57 1 0 57 58 1 0 3 59 1 0 14 3 1 0 13 5 1 0 21 8 1 0 20 15 1 0 27 22 1 0 40 25 1 0 32 28 1 0 39 28 1 0 36 31 1 0 1 60 1 0 1 61 1 0 1 62 1 0 2 63 1 0 2 64 1 0 4 65 1 0 4 66 1 0 5 67 1 0 6 68 1 0 6 69 1 0 10 70 1 0 10 71 1 0 11 72 1 0 11 73 1 0 13 74 1 0 13 75 1 0 14 76 1 0 14 77 1 0 16 78 1 0 17 79 1 0 18 80 1 0 19 81 1 0 21 82 1 0 24 83 1 0 27 84 1 0 29 85 1 0 29 86 1 0 30 87 1 0 30 88 1 0 32 89 1 0 34 90 1 0 35 91 1 0 36 92 1 0 36 93 1 0 37 94 1 0 39 95 1 0 41 96 1 0 41 97 1 0 41 98 1 0 45 99 1 0 45100 1 0 45101 1 0 46102 1 0 50103 1 0 50104 1 0 50105 1 0 51106 1 0 51107 1 0 52108 1 0 52109 1 0 52110 1 0 54111 1 0 54112 1 0 54113 1 0 58114 1 0 58115 1 0 58116 1 0 59117 1 0 M END

Standard InCHIKey	JXLYSJRDGCGARV-PHYWHDLESA-N
Standard InCHI	InChI=1S/C46H58N4O9/c1-8-42(54)23-28-24-45(40(52)57-6,36-30(15-19-49(25-28)26-42)29-13-10-11-14-33(29)47-36)32-21-31-34(22-35(32)56-5)48(4)38-44(31)17-20-50-18-12-16-43(9-2,37(44)50)39(59-27(3)51)46(38,55)41(53)58-7/h10-14,16,21-22,28,37-39,47,54-55H,8-9,15,17-20,23-26H2,1-7H3/t28?,37?,38-,39-,42+,43?,44-,45+,46+/m1/s1
SMILES	CCC1(CC2CC(C3=C(CCN(C2)C1)C4=CC=CC=C4N3)(C5=C(C=C6C(=C5)C78CCN9C7C(C=CC9)(C(C(C8N6C)(C(=O)OC)O)OC(=O)C)CC)OC)C(=O)OC)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	810.42	Volume:	821.262 ? Van der Waals volume.
Dense:	0.987	LogP:	3.913 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.395 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.945 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	10.0	Rigid Bonds:	48.0
TPSA:	154.1 ? Topological Polar Surface Area.	H-Bond Acceptor:	13.0
H-Bond Donor:	3.0	Rings:	9.0
Heavy Atoms:	13.0

MedChem Properties

QED Drug-Likeness Score:	0.18	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.152	Fsp³:	0.587
MCE-18:	269.589 ? 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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.187	Fluc inhibitor:	0.001 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.633 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.324 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.001	Promiscuous compounds:	0.397

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.107	MDCK Permeability:	-4.928
Pgp-inhibitor:	0.001	Pgp-substrate:	0.986
PAMPA:	0.068 ? 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%):	0.016	30% Bioavailability (F30%):	0.591
50% Bioavailability (F50%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.258	MRP1:	1.0
Plasma Protein Binding (PPB):	82.487%	Volume Distribution (VD):	0.462
Fu:	19.552% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.252
OATP1B3 inhibitor:	0.99	BCRP inhibitor:	0.739
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	1.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	1.0
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.812	CYP2C8-inhibitor:	0.002
HLM stability:	0.959 ? 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):

3.229

Half-life (T1/2):

2.261

ADMET: Toxicity

hERG Blockers:	0.879	hERG Blockers (10um):	0.606
Human Hepatotoxicity (H-HT):	0.827	Drug-induced Liver Injury (DILI):	0.11
AMES Toxicity:	0.438	Rat Oral Acute Toxicity:	0.899
Maximum Recommended Daily Dose:	0.998	Skin Sensitization:	0.049
Carcinogencity:	0.381	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.98
Drug-induced Neurotoxicity:	0.665	Ototoxicity:	0.991
Hematotoxicity:	0.225	Drug-induced Nephrotoxicity:	0.944
Genotoxicity:	0.999	RPMI-8226 Immunitoxicity:	0.111
A549 Cytotoxicity:	0.209	Hek293 Cytotoxicity:	0.851
BCF:	0.753 ? 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:	4.016 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.778 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.987 ? 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
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[ 3619437]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1002/btpr.97]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11738-010-0631-6]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.plaphy.2018.10.015]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1080/17429145.2017.1293852]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1186/1750-2187-3-9]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12628396]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	Hairy roots	n.a.	n.a.	PMID[19271765]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26285573]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6619887]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6631435]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7264679]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7264682]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7320741]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5881	Catharanthus roseus	Species	Apocynaceae	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

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 NPC324460 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	21078
0.1-0.2	28123
0.2-0.3	599
0.3-0.4	48
0.4-0.5	1
0.5-0.6	1
0.6-0.7	2
0.7-0.8	5
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC195788
1.0	High Similarity	NPC237901
0.9667	High Similarity	NPC485509
0.8268	Intermediate Similarity	NPC608514
0.8189	Intermediate Similarity	NPC277353
0.8189	Intermediate Similarity	NPC600057
0.7101	Intermediate Similarity	NPC260909
0.6985	Remote Similarity	NPC302688
0.6901	Remote Similarity	NPC489610
0.5918	Remote Similarity	NPC481036

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC324460 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4407
0.1-0.2	4688
0.2-0.3	37
0.3-0.4	4
0.4-0.5	0
0.5-0.6	0
0.6-0.7	4
0.7-0.8	5
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD8466	Phase 4
1.0	High Similarity	NPD8467	Approved
0.9667	High Similarity	NPD8465	Approved
0.8862	High Similarity	NPD8489	Phase 1
0.8125	Intermediate Similarity	NPD8364	Approved
0.7939	Intermediate Similarity	NPD8363	Approved
0.7939	Intermediate Similarity	NPD8365	Clinical (unspecified phase)
0.7101	Intermediate Similarity	NPD8460	Phase 4
0.7059	Intermediate Similarity	NPD8425	Approved
0.7059	Intermediate Similarity	NPD8426	Phase 4
0.6985	Remote Similarity	NPD8428	Approved
0.6985	Remote Similarity	NPD8429	Phase 4
0.6901	Remote Similarity	NPD8459	Approved
0.6783	Remote Similarity	NPD8427	Approved

Bioactivity similarity

Similar Natural Products in NPASS

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

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data