NPASS Compound

Natural Product: NPC162495

Natural Product ID	NPC162495
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	LRWLAXJSFDAHQE-NGOYXVJFSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL502338
PubChem CID	44559844
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0003494] Rhamnofolane and daphnane 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 98103 0 0 0 0 0 0 0 0999 V2000 10.4544 -2.9595 1.0514 C 0 0 0 0 0 0 0 0 0 0 0 0 10.8854 -2.3382 -0.2388 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5856 -0.9086 -0.3928 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1695 -0.4951 -0.4424 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3163 -0.8008 0.7157 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8905 -0.2668 0.5275 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9004 1.2113 0.3818 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4661 1.7366 0.2513 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7936 1.1477 -0.9553 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3658 1.6829 -1.0966 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5249 1.3523 0.0992 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3965 -0.1137 0.3462 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5515 -0.4458 1.5536 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1926 0.1045 1.3309 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9037 -0.6285 1.2987 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2353 -0.0426 1.0747 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0557 -0.1062 2.1975 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0671 0.7867 1.8346 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3488 1.9083 1.1406 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1191 1.3077 0.8750 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9751 2.2514 -0.1936 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7551 1.0444 -1.1060 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0484 -0.2445 -0.3671 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8364 -0.7494 0.0470 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9332 0.0511 0.7972 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.6230 -1.1090 1.4286 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.3722 -2.4165 1.1010 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6792 -1.7639 0.8287 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9853 -1.7657 -0.5948 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.1189 -0.9982 -1.5082 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.6609 -1.2115 -1.3508 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1040 -1.1463 -2.7042 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0478 -1.3449 -3.5851 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3291 -1.5621 -2.8934 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3285 -2.0960 -3.3878 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9047 -1.3604 -5.0898 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5388 0.3064 -1.5708 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.3114 -1.3171 -0.7714 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7710 -2.4085 1.7004 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4098 -2.2283 3.0455 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3448 1.1420 -1.6256 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2246 3.0874 2.0175 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0370 3.5609 2.3307 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4345 3.7521 2.5535 C 0 0 0 0 0 0 0 0 0 0 0 0 11.3511 -3.5319 1.4684 H 0 0 0 0 0 0 0 0 0 0 0 0 10.2112 -2.2512 1.8499 H 0 0 0 0 0 0 0 0 0 0 0 0 9.6218 -3.6861 0.9437 H 0 0 0 0 0 0 0 0 0 0 0 0 11.9944 -2.5093 -0.3747 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3584 -2.9466 -1.0489 H 0 0 0 0 0 0 0 0 0 0 0 0 11.1137 -0.5278 -1.3364 H 0 0 0 0 0 0 0 0 0 0 0 0 11.1226 -0.3128 0.4144 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1188 0.6108 -0.6657 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6779 -0.9492 -1.3549 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7184 -0.3843 1.6495 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1862 -1.9225 0.8620 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2431 -0.6028 1.3358 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5552 -0.7312 -0.4365 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4842 1.5684 -0.5182 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3747 1.7366 1.2387 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9430 1.4483 1.1851 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5557 2.8313 0.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3766 1.4664 -1.8431 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7987 0.0544 -0.9208 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9501 1.2863 -2.0432 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4718 2.7759 -1.2287 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9631 1.8857 0.9739 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5075 1.7699 -0.1003 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4197 -0.5830 0.4319 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9595 -0.5782 -0.5701 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0260 -0.0478 2.4632 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5516 -1.5467 1.6485 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0644 1.1697 1.1843 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8323 -1.7009 1.4410 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6756 1.1123 2.6839 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3609 3.0812 -0.6157 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0164 2.5621 -0.1378 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4255 1.2049 -1.9755 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7444 0.8011 0.5603 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6787 -0.9912 2.5615 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0090 -2.8347 -0.9616 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5004 -2.2742 -1.0335 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0783 -0.9680 -2.9402 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9223 -0.9146 -5.3233 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8375 -2.4284 -5.4451 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7556 -0.8978 -5.5861 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7094 0.6424 -2.4777 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7380 -1.7486 -1.5474 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9212 -3.4640 1.4464 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6791 -1.8007 1.5461 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7733 -1.3789 3.4148 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7247 0.2614 -1.4014 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8308 2.0935 -1.2864 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3110 1.2684 -2.7504 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1564 3.0794 1.9406 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8893 4.4278 2.9738 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3112 3.6563 1.8842 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6385 3.2941 3.5483 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1895 4.8188 2.7349 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 2 0 16 15 1 1 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 19 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 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 32 33 2 0 33 34 1 0 34 35 2 0 33 36 1 0 30 37 1 6 29 38 1 0 28 39 1 1 39 40 1 0 22 41 1 0 19 42 1 1 42 43 2 0 42 44 1 0 20 16 1 0 31 23 1 0 24 16 1 0 28 26 1 0 34 30 1 0 25 18 1 0 1 45 1 0 1 46 1 0 1 47 1 0 2 48 1 0 2 49 1 0 3 50 1 0 3 51 1 0 4 52 1 0 4 53 1 0 5 54 1 0 5 55 1 0 6 56 1 0 6 57 1 0 7 58 1 0 7 59 1 0 8 60 1 0 8 61 1 0 9 62 1 0 9 63 1 0 10 64 1 0 10 65 1 0 11 66 1 0 11 67 1 0 12 68 1 0 12 69 1 0 13 70 1 0 13 71 1 0 14 72 1 0 15 73 1 0 18 74 1 1 21 75 1 0 21 76 1 0 22 77 1 6 25 78 1 6 26 79 1 1 29 80 1 6 31 81 1 1 32 82 1 0 36 83 1 0 36 84 1 0 36 85 1 0 37 86 1 0 38 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 43 94 1 0 43 95 1 0 44 96 1 0 44 97 1 0 44 98 1 0 M END

Standard InCHIKey	LRWLAXJSFDAHQE-NGOYXVJFSA-N
Standard InCHI	InChI=1S/C36H54O8/c1-6-7-8-9-10-11-12-13-14-15-16-17-18-19-34-42-29-27-30-33(22-37,41-30)31(39)35(40)26(20-24(4)28(35)38)36(27,44-34)25(5)21-32(29,43-34)23(2)3/h18-20,25-27,29-31,37,39-40H,2,6-17,21-22H2,1,3-5H3/b19-18+/t25-,26-,27-,29-,30+,31-,32-,33+,34-,35-,36+/m1/s1
SMILES	CCCCCCCCCCCCC/C=C/[C@@]12O[C@H]3[C@@](O1)(C[C@H]([C@@]1(O2)[C@H]3[C@@H]2O[C@@]2([C@H]([C@]2([C@H]1C=C(C2=O)C)O)O)CO)C)C(=C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	614.38	Volume:	639.649 ? Van der Waals volume.
Dense:	0.96	LogP:	6.279 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.484 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.849 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	15.0	Rigid Bonds:	27.0
TPSA:	117.98 ? Topological Polar Surface Area.	H-Bond Acceptor:	8.0
H-Bond Donor:	3.0	Rings:	6.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.127	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.531	Fsp³:	0.806
MCE-18:	99.508 ? 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:	0.544	Fluc inhibitor:	0.003 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.002 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.004 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.147	Promiscuous compounds:	0.24

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.081	MDCK Permeability:	-4.673
Pgp-inhibitor:	0.0	Pgp-substrate:	0.001
PAMPA:	0.002 ? 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):	0.141
20% Bioavailability (F20%):	0.955	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.132	MRP1:	0.999
Plasma Protein Binding (PPB):	98.074%	Volume Distribution (VD):	0.615
Fu:	1.847% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.045
BSEP inhibitor:	0.992

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.59
CYP2C19-inhibitor:	0.119	CYP2C19-substrate:	0.174
CYP2C9-inhibitor:	0.716	CYP2C9-substrate:	0.003
CYP2D6-inhibitor:	0.256	CYP2D6-substrate:	0.542
CYP3A4-inhibitor:	0.037	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.323 ? 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):

4.757

Half-life (T1/2):

1.061

ADMET: Toxicity

hERG Blockers:	0.098	hERG Blockers (10um):	0.443
Human Hepatotoxicity (H-HT):	0.456	Drug-induced Liver Injury (DILI):	0.34
AMES Toxicity:	0.88	Rat Oral Acute Toxicity:	0.627
Maximum Recommended Daily Dose:	0.379	Skin Sensitization:	1.0
Carcinogencity:	0.624	Eye Corrosion:	0.004
Eye Irritation:	0.794	Respiratory Toxicity:	0.736
Drug-induced Neurotoxicity:	0.198	Ototoxicity:	0.552
Hematotoxicity:	0.516	Drug-induced Nephrotoxicity:	0.521
Genotoxicity:	0.004	RPMI-8226 Immunitoxicity:	0.353
A549 Cytotoxicity:	0.985	Hek293 Cytotoxicity:	0.953
BCF:	1.913 ? 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:	5.689 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.777 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	6.706 ? 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
NPO32646	synaptolepis kirkii	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11000015]
NPO33116	synaptolepis retusa	Species	Thymelaeaceae	Eukaryota	roots	n.a.	n.a.	PMID[3210015]
NPO32646	synaptolepis kirkii	Species	Thymelaeaceae	Eukaryota	roots	n.a.	n.a.	PMID[3210015]
NPO33116	synaptolepis retusa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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	10
Survival	2

Activity Type	# Activity
Organism	12

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
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	0.02	nmol	PMID[17822299]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	50.0	/nmol	DOI[10.6019/CHEMBL1201861]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	94.0	%	DOI[10.6019/CHEMBL1201861]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	6.0	%	PMID[19361168]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	100.0	%	PMID[19433363]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	69.0	%	PMID[19433363]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	4.7	n.a.	PMID[19433363]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	0.13	n.a.	PMID[19433363]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	9.7	n.a.	PMID[19433363]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	2.9	n.a.	PMID[22142538]
NPT32	Organism	Mus musculus	Mus musculus	Survival	=	94.0	%	PMID[22142538]
NPT32	Organism	Mus musculus	Mus musculus	Survival	=	100.0	%	PMID[12088423]

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 NPC162495 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	16894
0.1-0.2	31152
0.2-0.3	1699
0.3-0.4	36
0.4-0.5	25
0.5-0.6	16
0.6-0.7	20
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	4
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9	High Similarity	NPC474508
0.9	High Similarity	NPC473485
0.9	High Similarity	NPC171411
0.9	High Similarity	NPC485701
0.8857	High Similarity	NPC251564
0.8857	High Similarity	NPC477189
0.7692	Intermediate Similarity	NPC475139
0.7632	Intermediate Similarity	NPC180902
0.726	Intermediate Similarity	NPC475273
0.726	Intermediate Similarity	NPC168849
0.726	Intermediate Similarity	NPC217901
0.726	Intermediate Similarity	NPC611341
0.7	Intermediate Similarity	NPC182266
0.7	Intermediate Similarity	NPC475154
0.7	Intermediate Similarity	NPC485700
0.6962	Remote Similarity	NPC485693
0.6875	Remote Similarity	NPC223356
0.6875	Remote Similarity	NPC298697
0.6875	Remote Similarity	NPC475500
0.6875	Remote Similarity	NPC100017
0.6875	Remote Similarity	NPC481742
0.6835	Remote Similarity	NPC475314
0.6835	Remote Similarity	NPC102997
0.679	Remote Similarity	NPC75831
0.679	Remote Similarity	NPC471137
0.6707	Remote Similarity	NPC471136
0.6707	Remote Similarity	NPC116727
0.6707	Remote Similarity	NPC39509
0.6627	Remote Similarity	NPC481744
0.6627	Remote Similarity	NPC481743
0.6625	Remote Similarity	NPC476091
0.6264	Remote Similarity	NPC486153
0.622	Remote Similarity	NPC324104
0.622	Remote Similarity	NPC473548
0.6173	Remote Similarity	NPC475606
0.5978	Remote Similarity	NPC92598
0.5978	Remote Similarity	NPC43304
0.5978	Remote Similarity	NPC481753
0.5978	Remote Similarity	NPC477188
0.5978	Remote Similarity	NPC477190
0.587	Remote Similarity	NPC68282
0.5789	Remote Similarity	NPC101786
0.567	Remote Similarity	NPC481773
0.5426	Remote Similarity	NPC164150
0.5426	Remote Similarity	NPC481754
0.5376	Remote Similarity	NPC475389
0.5258	Remote Similarity	NPC130886
0.5238	Remote Similarity	NPC69240
0.5227	Remote Similarity	NPC476078
0.5222	Remote Similarity	NPC473838
0.5152	Remote Similarity	NPC481774

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC162495 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6695
0.1-0.2	2419
0.2-0.3	36
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