NPASS Compound

Natural Product: NPC470029

Natural Product ID	NPC470029
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	NNFJPOSVDKIWPO-TWYTXGPDSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1651284
PubChem CID	53319991
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 [CHEMONTID:0001687] Cucurbitacin 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 3D 105112 0 0 0 0 0 0 0 0999 V2000 -4.1735 -3.9298 0.5638 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3154 -2.4933 0.1972 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7904 -2.1667 0.4204 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0733 -0.6716 0.2222 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5873 -0.3360 -1.1299 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2182 -0.1067 -0.9204 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0094 -0.1358 0.4508 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5395 -1.5047 0.9445 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0619 -1.5060 0.8899 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6207 -1.9010 -0.4717 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1067 -1.8164 -0.7126 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4085 -0.8947 0.3604 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4035 -1.5038 1.1027 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7463 -0.3187 0.4825 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3844 0.6012 1.4242 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8298 0.0358 1.4532 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3984 0.2236 0.0961 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4303 0.5169 -1.0266 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9858 0.3330 -0.7853 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2116 1.6646 -0.6220 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1106 1.5956 0.3956 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5020 0.2270 0.3129 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6894 -0.0389 1.1874 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9052 0.7784 0.8799 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7535 1.6812 -0.1696 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3827 0.1749 2.6554 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9046 -0.3468 -2.2136 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6780 1.9413 -1.5233 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3397 1.2017 0.1155 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5680 1.1847 -0.1555 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0610 0.6379 1.4521 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4435 0.2135 1.2709 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9282 -0.2065 -0.0588 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8401 -0.5850 -1.0147 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5659 -0.4057 -0.6011 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7792 0.7673 -0.6073 O 0 0 0 0 0 0 0 0 0 0 0 0 9.2865 1.2341 1.7905 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8946 1.8147 2.0977 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5766 -2.4347 1.9820 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2183 0.0799 1.0536 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2709 0.7974 -1.7909 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6919 0.2969 -2.1215 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6626 0.9973 -3.2214 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2531 2.0090 -1.2209 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7137 2.6268 -0.1353 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4049 2.0079 0.6717 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4304 4.0707 0.1683 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8131 -4.1810 1.4586 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6247 -4.5248 -0.2787 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1874 -4.3262 0.7373 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1300 -2.3576 -0.9086 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4145 -2.6898 -0.3097 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9984 -2.3881 1.4811 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1282 -0.5641 0.4373 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6766 -1.2641 -1.8037 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8428 -1.5738 2.0335 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9279 -2.9162 -0.7033 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1834 -1.2433 -1.1882 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0277 -1.4056 -1.7453 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3089 -2.8127 -0.7575 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9573 -2.4288 0.7567 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2626 -1.6287 2.2085 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9933 0.5918 2.4605 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6147 1.6312 1.1256 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8338 -0.9917 1.8250 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2986 0.6561 2.2587 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9077 -0.7634 -0.1381 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5835 -0.2522 -1.6410 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8605 2.5263 -0.5136 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7293 1.8101 -1.6391 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3023 1.9062 1.4070 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6109 2.4009 0.0401 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9951 0.3277 -0.7157 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2412 1.4093 1.7571 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8413 1.2697 -1.0446 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5162 1.2893 2.8175 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3373 -0.0050 2.9309 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1402 -0.2948 3.2914 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8189 0.0793 -2.6529 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1666 -1.3691 -1.8337 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1065 -0.4884 -2.9508 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8827 2.6421 -0.6974 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9025 2.2722 -2.2351 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6327 1.9565 -2.1338 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5392 1.1710 -0.3699 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3780 -0.1746 1.6056 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6876 -0.6616 1.9813 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5491 -1.1583 0.0794 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9831 -0.0254 -1.9715 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9208 -1.6652 -1.3379 H 0 0 0 0 0 0 0 0 0 0 0 0 9.8598 1.4951 0.0423 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1650 0.8438 1.9507 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2147 2.5589 1.5451 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0359 -1.9114 2.7896 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4291 -2.9323 2.5337 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9354 -3.2492 1.5862 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2986 1.0894 -2.5715 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5469 -0.4952 -2.8820 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1661 -0.1810 -1.2456 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7088 1.5505 -3.1183 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5168 0.0119 -3.6525 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3643 1.6544 -3.7755 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8855 4.5710 -0.6319 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8243 4.1587 1.1147 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3584 4.6394 0.3731 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 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 23 26 1 0 18 27 1 0 18 28 1 0 17 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 1 0 33 36 1 0 32 37 1 0 31 38 1 0 9 39 1 0 7 40 1 0 5 41 1 0 41 42 1 0 41 43 1 0 41 44 1 0 44 45 1 0 45 46 2 0 45 47 1 0 8 2 1 0 40 4 1 0 24 7 1 0 23 9 1 0 14 12 1 0 22 12 1 0 19 14 1 0 35 30 1 0 1 48 1 0 1 49 1 0 1 50 1 0 2 51 1 0 3 52 1 0 3 53 1 0 4 54 1 0 5 55 1 0 8 56 1 0 10 57 1 0 10 58 1 0 11 59 1 0 11 60 1 0 13 61 1 0 13 62 1 0 15 63 1 0 15 64 1 0 16 65 1 0 16 66 1 0 17 67 1 0 19 68 1 0 20 69 1 0 20 70 1 0 21 71 1 0 21 72 1 0 22 73 1 0 24 74 1 0 25 75 1 0 26 76 1 0 26 77 1 0 26 78 1 0 27 79 1 0 27 80 1 0 27 81 1 0 28 82 1 0 28 83 1 0 28 84 1 0 30 85 1 0 31 86 1 0 32 87 1 0 33 88 1 0 34 89 1 0 34 90 1 0 36 91 1 0 37 92 1 0 38 93 1 0 39 94 1 0 39 95 1 0 39 96 1 0 42 97 1 0 42 98 1 0 42 99 1 0 43100 1 0 43101 1 0 43102 1 0 47103 1 0 47104 1 0 47105 1 0 M END

Standard InCHIKey	NNFJPOSVDKIWPO-TWYTXGPDSA-N
Standard InCHI	InChI=1S/C37H58O10/c1-18-15-21-28(32(5,6)45-19(2)38)47-37(46-21)27(18)33(7)13-14-36-17-35(36)12-11-24(44-29-26(41)25(40)20(39)16-43-29)31(3,4)22(35)9-10-23(36)34(33,8)30(37)42/h18,20-30,39-42H,9-17H2,1-8H3/t18-,20+,21+,22+,23+,24+,25+,26-,27-,28+,29+,30-,33-,34-,35-,36+,37+/m1/s1
SMILES	CC1CC2C(OC3(C1C4(CCC56CC57CCC(C(C7CCC6C4(C3O)C)(C)C)OC8C(C(C(CO8)O)O)O)C)O2)C(C)(C)OC(=O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	662.4	Volume:	665.322 ? Van der Waals volume.
Dense:	0.996	LogP:	2.91 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.475 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.21 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	37.0
TPSA:	144.14 ? Topological Polar Surface Area.	H-Bond Acceptor:	10.0
H-Bond Donor:	4.0	Rings:	8.0
Heavy Atoms:	10.0

MedChem Properties

QED Drug-Likeness Score:	0.26	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.386	Fsp³:	0.973
MCE-18:	216.904 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.324	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:	0.039 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.074	Promiscuous compounds:	0.004

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.681	MDCK Permeability:	-5.069
Pgp-inhibitor:	0.007	Pgp-substrate:	0.431
PAMPA:	0.91 ? 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):	0.021
20% Bioavailability (F20%):	0.059	30% Bioavailability (F30%):	0.521
50% Bioavailability (F50%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.016	MRP1:	1.0
Plasma Protein Binding (PPB):	54.597%	Volume Distribution (VD):	-0.349
Fu:	42.861% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.003
OATP1B3 inhibitor:	0.84	BCRP inhibitor:	0.003
BSEP inhibitor:	0.962

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.989	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.964	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.197	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.501	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.974	CYP2C8-inhibitor:	0.012
HLM stability:	0.853 ? 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):

5.038

Half-life (T1/2):

2.254

ADMET: Toxicity

hERG Blockers:	0.134	hERG Blockers (10um):	0.507
Human Hepatotoxicity (H-HT):	0.358	Drug-induced Liver Injury (DILI):	0.157
AMES Toxicity:	0.483	Rat Oral Acute Toxicity:	0.395
Maximum Recommended Daily Dose:	0.379	Skin Sensitization:	0.347
Carcinogencity:	0.05	Eye Corrosion:	0.0
Eye Irritation:	0.001	Respiratory Toxicity:	0.045
Drug-induced Neurotoxicity:	0.563	Ototoxicity:	0.968
Hematotoxicity:	0.021	Drug-induced Nephrotoxicity:	0.029
Genotoxicity:	0.021	RPMI-8226 Immunitoxicity:	0.093
A549 Cytotoxicity:	0.056	Hek293 Cytotoxicity:	0.681
BCF:	2.122 ? 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:	5.206 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.491 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	6.051 ? 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
NPO525	Actaea racemosa	Species	Ranunculaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[11824572]
NPO525	Actaea racemosa	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16124775]
NPO525	Actaea racemosa	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16562825]
NPO525	Actaea racemosa	Species	Ranunculaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21082802]
NPO525	Actaea racemosa	Species	Ranunculaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[21082802]
NPO525	Actaea racemosa	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO525	Actaea racemosa	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO525	Actaea racemosa	Species	Ranunculaceae	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
Activity	2
EC50	1

Activity Type	# Activity
Others	3

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
NPT2	Others	Unspecified	n.a.	Activity	=	271.0	%	DrugMatrix in vivo data: Pathology
NPT2	Others	Unspecified	n.a.	Activity	=	289.0	%	PMID[15497933]
NPT2	Others	Unspecified	n.a.	EC50	=	26000.0	nM	PMID[19897281]

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 NPC470029 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	22496
0.1-0.2	24742
0.2-0.3	2485
0.3-0.4	88
0.4-0.5	28
0.5-0.6	6
0.6-0.7	6
0.7-0.8	0
0.8-0.85	2
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8571	High Similarity	NPC476839
0.8571	High Similarity	NPC476838
0.8026	Intermediate Similarity	NPC470028
0.8025	Intermediate Similarity	NPC310138
0.7901	Intermediate Similarity	NPC114700
0.7625	Intermediate Similarity	NPC476512
0.7045	Intermediate Similarity	NPC478614
0.6824	Remote Similarity	NPC134967
0.6667	Remote Similarity	NPC476510
0.6548	Remote Similarity	NPC233649
0.6264	Remote Similarity	NPC478610
0.6235	Remote Similarity	NPC227879
0.6235	Remote Similarity	NPC208333
0.593	Remote Similarity	NPC476513
0.5795	Remote Similarity	NPC92299
0.5208	Remote Similarity	NPC55384
0.5185	Remote Similarity	NPC228059
0.5165	Remote Similarity	NPC478630
0.5055	Remote Similarity	NPC478613

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC470029 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7149
0.1-0.2	1967
0.2-0.3	33
0.3-0.4	1
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