NPASS Compound

Natural Product: NPC483061

Natural Product ID	NPC483061
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	PLDKIKPDXFIXLY-VQTWSDOUSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

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 93 95 0 0 0 0 0 0 0 0999 V2000 1.6168 5.3468 -0.3662 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8876 4.1163 0.4845 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8958 3.2826 0.7729 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0797 2.0972 1.5733 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7014 0.7536 1.0602 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7710 0.7157 0.7599 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2066 0.7066 -0.6521 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2258 1.8096 -0.9773 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4183 1.6756 -0.1318 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8950 2.5353 0.7328 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1447 2.2411 1.5295 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2721 3.8522 1.0226 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7714 -0.6210 -1.0316 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8999 -1.5860 -1.2718 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6450 -2.8607 -1.0647 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0296 -2.4742 -1.5313 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0435 -3.2764 -0.7484 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4565 -2.8554 -1.0055 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8742 -4.7200 -1.1076 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7524 -3.1314 0.6065 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0651 -1.0991 -1.1991 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4869 -1.3725 -1.6528 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1848 -2.2587 -2.2089 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0846 0.0076 -1.3455 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2200 0.1239 -2.2633 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1050 -0.7503 -2.0617 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5004 1.0487 -3.3442 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5649 2.5027 -3.0375 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5851 0.8123 -4.5502 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0595 0.8860 -1.5873 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1149 1.6861 -2.4434 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5544 0.0345 0.1036 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0125 0.4729 0.1555 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6644 -1.4217 0.5329 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2875 -1.6484 1.8626 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2994 -3.1723 2.0697 C 0 0 2 0 0 0 0 0 0 0 0 0 2.9121 -3.5030 3.4085 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2175 -4.1417 4.3382 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3208 -3.1210 3.7294 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0726 -3.7874 1.1093 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2772 3.9472 0.9413 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9864 5.0264 -1.2245 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0154 6.0777 0.2146 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5325 5.7896 -0.7512 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0678 3.5918 0.3501 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3885 2.2676 2.4838 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0686 2.1180 2.0693 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7270 0.1123 2.0204 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2074 1.6643 1.2097 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3241 -0.0777 1.3391 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8120 2.7986 -0.9285 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5003 1.6627 -2.0791 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9946 0.7401 -0.2298 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9429 2.9978 1.3276 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8761 2.1816 2.6081 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4792 1.2363 1.2255 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0873 4.6141 1.0019 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7561 3.8254 2.0201 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5115 4.1584 0.2902 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2199 -3.6923 -1.6509 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6978 -3.0806 0.0238 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0832 -2.6483 -2.6209 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6362 -2.4737 -2.0116 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1357 -3.7314 -0.8409 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7677 -2.0910 -0.2411 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3505 -4.9005 -2.0619 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8719 -5.2490 -1.1927 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3382 -5.2811 -0.2997 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9649 -3.9880 1.0442 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5321 0.7700 -3.7611 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2985 2.7966 -2.0088 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5625 2.9584 -3.3329 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8521 3.0593 -3.7115 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0953 1.7432 -4.8657 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8393 0.0232 -4.3550 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1673 0.4317 -5.4377 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6553 -0.4327 0.0712 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3315 1.1251 -0.6453 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2190 0.8382 1.1881 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6897 -1.9531 0.5132 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3182 -1.9736 -0.2100 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3756 -1.3582 1.8853 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8503 -1.2033 2.7385 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2570 -3.5605 2.1101 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1965 -4.4370 4.1520 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6666 -4.3684 5.2824 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0436 -3.8901 3.3705 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6062 -2.1800 3.2605 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4615 -3.0202 4.8282 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0292 -3.7235 1.3415 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7992 4.9541 0.8895 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3184 3.6770 2.0244 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8562 3.2213 0.3661 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 1 8 9 1 0 9 10 2 3 10 11 1 0 10 12 1 0 7 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 17 19 1 0 17 20 1 0 16 21 1 0 14 22 1 0 22 23 2 0 22 24 1 0 24 25 1 6 25 26 2 0 25 27 1 0 27 28 1 0 27 29 1 0 24 30 1 0 30 31 2 0 24 32 1 0 32 33 1 6 32 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 2 0 37 39 1 0 36 40 1 0 2 41 1 0 32 5 1 0 30 7 1 0 21 13 1 0 1 42 1 0 1 43 1 0 1 44 1 0 3 45 1 0 4 46 1 0 4 47 1 0 5 48 1 1 6 49 1 0 6 50 1 0 8 51 1 0 8 52 1 0 9 53 1 0 11 54 1 0 11 55 1 0 11 56 1 0 12 57 1 0 12 58 1 0 12 59 1 0 15 60 1 0 15 61 1 0 16 62 1 6 18 63 1 0 18 64 1 0 18 65 1 0 19 66 1 0 19 67 1 0 19 68 1 0 20 69 1 0 27 70 1 0 28 71 1 0 28 72 1 0 28 73 1 0 29 74 1 0 29 75 1 0 29 76 1 0 33 77 1 0 33 78 1 0 33 79 1 0 34 80 1 0 34 81 1 0 35 82 1 0 35 83 1 0 36 84 1 1 38 85 1 0 38 86 1 0 39 87 1 0 39 88 1 0 39 89 1 0 40 90 1 0 41 91 1 0 41 92 1 0 41 93 1 0 M END

Standard InCHIKey	PLDKIKPDXFIXLY-VQTWSDOUSA-N
Standard InCHI	InChI=1S/C35H52O6/c1-20(2)12-13-24-19-34(17-14-21(3)4)30-25(18-27(41-30)32(9,10)40)29(38)35(31(34)39,28(37)23(7)8)33(24,11)16-15-26(36)22(5)6/h12,14,23-24,26-27,36,40H,5,13,15-19H2,1-4,6-11H3/t24-,26+,27-,33+,34+,35-/m0/s1
SMILES	CC(=CC[C@H]1C[C@]2(CC=C(C)C)C3=C(C[C@@H](C(C)(C)O)O3)C(=O)[C@@](C(=O)C(C)C)(C2=O)[C@]1(C)CC[C@H](C(=C)C)O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	568.38	Volume:	622.533 ? Van der Waals volume.
Dense:	0.913	LogP:	5.326 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.261 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.028 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	11.0	Rigid Bonds:	20.0
TPSA:	100.9 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	2.0	Rings:	3.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.215	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.189	Fsp³:	0.686
MCE-18:	73.831 ? 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:	1	PAINS Alert:	0
Colloidal aggregators:	0.939	Fluc inhibitor:	0.005 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.038 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.019 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.526	Promiscuous compounds:	0.151

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.742	MDCK Permeability:	-4.712
Pgp-inhibitor:	0.001	Pgp-substrate:	0.467
PAMPA:	0.781 ? 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%):	0.0	30% Bioavailability (F30%):	0.0
50% Bioavailability (F50%):	0.168

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.058	MRP1:	0.999
Plasma Protein Binding (PPB):	69.134%	Volume Distribution (VD):	0.067
Fu:	32.62% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.886
OATP1B3 inhibitor:	0.333	BCRP inhibitor:	0.024
BSEP inhibitor:	0.984

ADMET: Metabolism

CYP1A2-inhibitor:	0.462	CYP1A2-substrate:	0.807
CYP2C19-inhibitor:	0.997	CYP2C19-substrate:	0.007
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.001	CYP2D6-substrate:	0.517
CYP3A4-inhibitor:	0.99	CYP3A4-substrate:	0.999
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.998
HLM stability:	0.821 ? 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):

6.74

Half-life (T1/2):

0.793

ADMET: Toxicity

hERG Blockers:	0.032	hERG Blockers (10um):	0.174
Human Hepatotoxicity (H-HT):	0.898	Drug-induced Liver Injury (DILI):	0.366
AMES Toxicity:	0.64	Rat Oral Acute Toxicity:	0.423
Maximum Recommended Daily Dose:	0.506	Skin Sensitization:	0.992
Carcinogencity:	0.966	Eye Corrosion:	0.0
Eye Irritation:	0.062	Respiratory Toxicity:	0.647
Drug-induced Neurotoxicity:	0.269	Ototoxicity:	0.706
Hematotoxicity:	0.748	Drug-induced Nephrotoxicity:	0.986
Genotoxicity:	0.999	RPMI-8226 Immunitoxicity:	0.05
A549 Cytotoxicity:	0.135	Hek293 Cytotoxicity:	0.202
BCF:	1.879 ? 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:	4.85 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.679 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	6.192 ? 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
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11240-015-0798-z]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.fitote.2006.01.011]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jarmap.2018.11.004]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.plaphy.2005.07.013]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1078/0176-1617-00195]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1155/2014/609649]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10757735]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14735439]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	callus	n.a.	PMID[15715262]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18220354]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28445039]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	Roots	n.a.	n.a.	PMID[30024167]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32560389]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36336219]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38217369]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4391	Hypericum perforatum	Species	Hypericaceae	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

Activity Type	# Activity
Individual protein	1
Cell line	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT204	Individual protein	Acetylcholinesterase	Homo sapiens	IC50	=	26430.0	nM	PMID[28445039]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT659	Cell line	SMMC-7721	Homo sapiens	IC50	=	9100.0	nM	PMID[28445039]

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 NPC483061 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	19345
0.1-0.2	28174
0.2-0.3	2223
0.3-0.4	51
0.4-0.5	25
0.5-0.6	21
0.6-0.7	14
0.7-0.8	0
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC483062
0.806	Intermediate Similarity	NPC483057
0.803	Intermediate Similarity	NPC483060
0.7042	Intermediate Similarity	NPC483052
0.7042	Intermediate Similarity	NPC483051
0.6714	Remote Similarity	NPC471331
0.6714	Remote Similarity	NPC99657
0.6714	Remote Similarity	NPC203388
0.6528	Remote Similarity	NPC483059
0.6522	Remote Similarity	NPC472733
0.6522	Remote Similarity	NPC472734
0.625	Remote Similarity	NPC483076
0.625	Remote Similarity	NPC483078
0.6164	Remote Similarity	NPC483064
0.6164	Remote Similarity	NPC483063
0.6081	Remote Similarity	NPC471330
0.6081	Remote Similarity	NPC472687
0.6076	Remote Similarity	NPC471333
0.6076	Remote Similarity	NPC471332
0.5972	Remote Similarity	NPC483058
0.5949	Remote Similarity	NPC47466
0.5949	Remote Similarity	NPC116274
0.5915	Remote Similarity	NPC27105
0.589	Remote Similarity	NPC472732
0.589	Remote Similarity	NPC472731
0.5616	Remote Similarity	NPC472729
0.5616	Remote Similarity	NPC472730
0.561	Remote Similarity	NPC483077
0.5513	Remote Similarity	NPC328997
0.5513	Remote Similarity	NPC294050
0.5513	Remote Similarity	NPC610705
0.5405	Remote Similarity	NPC38885
0.5342	Remote Similarity	NPC177680
0.5342	Remote Similarity	NPC153776
0.5263	Remote Similarity	NPC483080
0.5263	Remote Similarity	NPC472728
0.5263	Remote Similarity	NPC472727
0.5065	Remote Similarity	NPC21681
0.5062	Remote Similarity	NPC483055
0.5062	Remote Similarity	NPC483056

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC483061 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7213
0.1-0.2	1915
0.2-0.3	22
0.3-0.4	0
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