NPASS Compound

Natural Product: NPC488456

Natural Product ID	NPC488456
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	YPYLGRHDOPMGHC-QLUPERJSSA-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]

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 108113 0 0 0 0 0 0 0 0999 V2000 4.0811 2.1441 0.2686 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4727 1.6385 0.1387 C 0 0 1 0 0 0 0 0 0 0 0 0 5.7892 0.4904 1.0601 C 0 0 2 0 0 0 0 0 0 0 0 0 7.3176 0.4207 1.1394 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7933 0.1678 -0.2799 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2167 1.1896 -1.2330 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7825 2.4497 -1.0491 O 0 0 0 0 0 0 0 0 0 0 0 0 8.4761 2.8829 -2.1568 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8246 1.2561 -1.1508 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7389 -0.6617 2.0329 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1083 -1.8208 1.9384 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0968 -1.9273 1.0025 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3166 -0.8389 0.5535 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0016 -1.1199 0.9795 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1859 -1.3994 -0.1110 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5969 -2.7819 -0.0479 C 0 0 1 0 0 0 0 0 0 0 0 0 1.9767 -3.0639 -1.4185 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9400 -1.9408 -1.7101 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6261 -0.6428 -1.5273 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9811 0.5515 -2.0957 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0624 1.1350 -1.4617 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2594 0.4903 -1.3450 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6286 0.2119 0.1062 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1202 0.0371 0.2348 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5161 -1.1532 -0.5582 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3028 -1.1026 -1.6210 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7908 0.1544 -2.0159 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0544 1.0252 -0.9040 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7793 1.3141 -0.1824 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8283 2.1329 -1.0419 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5822 3.2783 -1.7073 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2764 1.2767 -1.9556 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9861 0.4909 -0.0495 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1727 1.2381 0.0310 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.2619 0.3855 -0.5112 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.6235 0.6619 0.0262 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.6270 1.4548 1.3013 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.3390 1.2989 2.0542 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.1790 -0.0683 2.6669 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.3130 -0.3436 3.4133 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2998 1.7132 1.2863 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.7757 2.8130 0.9920 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3159 -0.5260 0.2724 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.3240 0.6043 -1.9095 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0213 -2.4506 -0.1349 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2875 -2.5462 0.8559 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3739 -3.5780 -0.8439 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9007 -4.8749 -0.4494 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1456 -0.4800 -0.2350 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5971 -2.1130 -3.0409 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3971 -4.2948 -1.5195 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5875 -3.7445 0.1262 O 0 0 0 0 0 0 0 0 0 0 0 0 8.8176 -0.4631 2.9927 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1438 -1.4270 3.7413 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5035 0.7152 3.1321 O 0 0 0 0 0 0 0 0 0 0 0 0 10.5541 0.9371 4.0543 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6272 1.6347 1.1657 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4564 2.0162 -0.6222 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0713 3.2290 0.5229 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1868 2.4622 0.4148 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3471 0.6771 2.0637 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7367 1.4187 1.4271 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8856 0.2161 -0.3574 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4884 -0.8402 -0.6448 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4849 0.8594 -2.2576 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8902 3.8860 -1.9249 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3591 2.2110 -2.3171 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8586 2.9945 -3.0687 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4038 -2.6338 2.5894 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3306 -0.9156 -0.5672 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7733 -1.3338 -1.0613 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7953 -2.8658 0.7210 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7776 -2.9103 -2.1625 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0547 -2.1234 -1.0858 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6074 -0.7585 -2.1507 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7504 0.3352 -3.1851 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7687 1.3811 -2.2038 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2246 -0.4753 -1.8696 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2959 1.1198 0.6871 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0592 -0.6580 0.4381 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3913 -0.1171 1.3078 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5349 -2.0168 -2.1352 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4857 1.9615 -1.3424 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0309 1.9564 0.7002 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0818 2.6155 -0.3901 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3130 3.6479 -0.9338 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8516 4.0876 -1.9460 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1004 2.9478 -2.6248 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0125 2.1175 -0.6615 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0288 -0.7026 -0.4166 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.2691 1.2325 -0.7024 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.5210 1.1819 1.9097 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4098 2.0122 2.9310 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3239 0.0222 3.3995 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9019 -0.8541 1.9714 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.0971 -0.5429 4.3643 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.6488 3.1731 1.2608 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.8230 -0.7907 -0.5554 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7534 1.4702 -2.1140 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5859 -5.4586 -1.3379 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0843 -4.7512 0.2987 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7402 -5.4106 0.0234 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3494 -2.3770 -3.1673 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6994 -4.7122 -2.3631 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9871 -3.9536 -0.7580 H 0 0 0 0 0 0 0 0 0 0 0 0 11.0418 0.0025 4.3636 H 0 0 0 0 0 0 0 0 0 0 0 0 11.2889 1.5951 3.5229 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1796 1.5402 4.9213 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 6 9 1 0 4 10 1 0 10 11 2 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 25 26 2 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 30 32 1 0 28 33 1 0 33 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 39 40 1 0 38 41 1 0 37 42 1 0 36 43 1 0 35 44 1 0 25 45 1 0 45 46 2 0 45 47 1 0 47 48 1 0 19 49 1 0 18 50 1 0 17 51 1 0 16 52 1 0 10 53 1 0 53 54 2 0 53 55 1 0 55 56 1 0 9 2 1 0 49 15 1 0 13 3 1 0 32 22 1 0 41 34 1 0 29 24 1 0 1 57 1 0 1 58 1 0 1 59 1 0 2 60 1 1 3 61 1 1 4 62 1 1 5 63 1 0 5 64 1 0 6 65 1 6 8 66 1 0 8 67 1 0 8 68 1 0 11 69 1 0 13 70 1 6 15 71 1 6 16 72 1 1 17 73 1 6 18 74 1 1 19 75 1 6 20 76 1 0 20 77 1 0 22 78 1 6 23 79 1 0 23 80 1 0 24 81 1 1 26 82 1 0 28 83 1 6 29 84 1 1 30 85 1 1 31 86 1 0 31 87 1 0 31 88 1 0 34 89 1 6 35 90 1 6 36 91 1 6 37 92 1 1 38 93 1 1 39 94 1 0 39 95 1 0 40 96 1 0 42 97 1 0 43 98 1 0 44 99 1 0 48100 1 0 48101 1 0 48102 1 0 50103 1 0 51104 1 0 52105 1 0 56106 1 0 56107 1 0 56108 1 0 M END

Standard InCHIKey	YPYLGRHDOPMGHC-QLUPERJSSA-N
Standard InCHI	InChI=1S/C35H52O21/c1-12-22-14(6-20(45-3)51-12)16(30(43)46-4)9-49-32(22)56-35-29(42)27(40)25(38)19(54-35)11-48-21-7-15-17(31(44)47-5)10-50-33(23(15)13(2)52-21)55-34-28(41)26(39)24(37)18(8-36)53-34/h9-10,12-15,18-29,32-42H,6-8,11H2,1-5H3/t12-,13-,14+,15+,18+,19+,20+,21+,22+,23+,24+,25+,26-,27-,28+,29+,32-,33-,34-,35-/m0/s1
SMILES	C[C@H]1[C@@H]2[C@H](C[C@H](OC)O1)C(=CO[C@H]2O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2C[C@@H]3C(=CO[C@H]([C@@H]3[C@H](C)O2)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)C(=O)OC)O1)O)O)O)C(=O)OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	808.3	Volume:	736.626 ? Van der Waals volume.
Dense:	1.097	LogP:	-0.142 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.512 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.563 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	13.0	Rigid Bonds:	36.0
TPSA:	286.51 ? Topological Polar Surface Area.	H-Bond Acceptor:	21.0
H-Bond Donor:	7.0	Rings:	6.0
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:	6.125	Fsp³:	0.829
MCE-18:	112.875 ? 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:	0.385	Fluc inhibitor:	0.334 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.078 ? 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:	0.428	Promiscuous compounds:	0.084

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.717	MDCK Permeability:	-5.42
Pgp-inhibitor:	0.0	Pgp-substrate:	0.636
PAMPA:	0.998 ? 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):	0.16
20% Bioavailability (F20%):	0.014	30% Bioavailability (F30%):	0.979
50% Bioavailability (F50%):	0.949

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.912
Plasma Protein Binding (PPB):	41.474%	Volume Distribution (VD):	-0.548
Fu:	53.122% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.002
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.071	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.012
HLM stability:	0.006 ? 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):

0.736

Half-life (T1/2):

4.292

ADMET: Toxicity

hERG Blockers:	0.005	hERG Blockers (10um):	0.026
Human Hepatotoxicity (H-HT):	0.602	Drug-induced Liver Injury (DILI):	1.0
AMES Toxicity:	0.996	Rat Oral Acute Toxicity:	0.019
Maximum Recommended Daily Dose:	0.018	Skin Sensitization:	1.0
Carcinogencity:	0.019	Eye Corrosion:	0.0
Eye Irritation:	0.001	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.003	Ototoxicity:	1.0
Hematotoxicity:	0.942	Drug-induced Nephrotoxicity:	0.993
Genotoxicity:	0.446	RPMI-8226 Immunitoxicity:	0.384
A549 Cytotoxicity:	0.96	Hek293 Cytotoxicity:	0.29
BCF:	0.323 ? 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:	2.746 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.461 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.607 ? 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
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[29140705]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12588	Cornus officinalis	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12588	Cornus officinalis	Species	Cornaceae	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	1

Activity Type	# Activity
Individual protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT38	Individual protein	Signal transducer and activator of transcription 3	Homo sapiens	IC50	>	100000.0	nM	PMID[29140705]

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 NPC488456 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	19117
0.1-0.2	26488
0.2-0.3	3707
0.3-0.4	412
0.4-0.5	79
0.5-0.6	31
0.6-0.7	9
0.7-0.8	0
0.8-0.85	3
0.85-0.9	3
0.9-0.95	2
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC488465
1.0	High Similarity	NPC488460
1.0	High Similarity	NPC488462
0.9375	High Similarity	NPC488471
0.9375	High Similarity	NPC488466
0.871	High Similarity	NPC470573
0.871	High Similarity	NPC120021
0.871	High Similarity	NPC216826
0.8451	Intermediate Similarity	NPC488467
0.8438	Intermediate Similarity	NPC488472
0.8438	Intermediate Similarity	NPC257424
0.7746	Intermediate Similarity	NPC488457
0.7746	Intermediate Similarity	NPC488464
0.7746	Intermediate Similarity	NPC488463
0.7123	Intermediate Similarity	NPC488470
0.6892	Remote Similarity	NPC488459
0.6842	Remote Similarity	NPC488461
0.6842	Remote Similarity	NPC488458
0.6625	Remote Similarity	NPC488468
0.6571	Remote Similarity	NPC231710
0.6571	Remote Similarity	NPC270908
0.6571	Remote Similarity	NPC65665
0.6486	Remote Similarity	NPC197541
0.6486	Remote Similarity	NPC118761
0.5972	Remote Similarity	NPC27687
0.5915	Remote Similarity	NPC35185
0.5915	Remote Similarity	NPC4899
0.5915	Remote Similarity	NPC177013
0.5904	Remote Similarity	NPC488469
0.5867	Remote Similarity	NPC41681
0.5775	Remote Similarity	NPC474730
0.5775	Remote Similarity	NPC117596
0.5769	Remote Similarity	NPC284929
0.5753	Remote Similarity	NPC37240
0.5714	Remote Similarity	NPC469543
0.5694	Remote Similarity	NPC255677
0.5694	Remote Similarity	NPC22149
0.5694	Remote Similarity	NPC306344
0.557	Remote Similarity	NPC267869
0.5556	Remote Similarity	NPC323472
0.5541	Remote Similarity	NPC106668
0.5526	Remote Similarity	NPC222062
0.5479	Remote Similarity	NPC307699
0.5479	Remote Similarity	NPC475928
0.5432	Remote Similarity	NPC86095
0.5405	Remote Similarity	NPC148270
0.5342	Remote Similarity	NPC170432
0.527	Remote Similarity	NPC298255
0.5181	Remote Similarity	NPC470683
0.5181	Remote Similarity	NPC470684
0.5181	Remote Similarity	NPC270737
0.5132	Remote Similarity	NPC61201
0.5067	Remote Similarity	NPC195510
0.5067	Remote Similarity	NPC13171
0.5062	Remote Similarity	NPC234304

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC488456 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6652
0.1-0.2	2420
0.2-0.3	73
0.3-0.4	5
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