NPASS Compound

Natural Product: NPC487395

Natural Product ID	NPC487395
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	VDCIZHNJZDCCAB-ORJPLPFJSA-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:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002106] Anthracyclines

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 105111 0 0 0 0 0 0 0 0999 V2000 -4.7845 0.5134 -5.1932 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8524 1.1114 -4.1797 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1508 0.6370 -2.7745 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1637 1.2955 -1.8655 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3803 0.9589 -0.3852 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.6518 0.3232 -0.1043 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7257 0.3469 -1.0043 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5613 1.0474 -2.3331 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.5531 2.5040 -2.0630 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6773 2.9643 -0.8997 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4070 3.4467 -3.0791 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3933 4.8251 -2.8542 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9013 -0.2583 -0.6922 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0780 -0.9103 0.5078 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0589 -0.9626 1.4226 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2165 -1.6534 2.7157 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2720 -1.6907 3.5415 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.4819 -2.2970 3.0334 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5020 -2.2417 2.1114 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.6933 -2.8585 2.4314 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.8757 -3.5192 3.6408 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8531 -3.5736 4.5628 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6603 -2.9610 4.2529 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6282 -3.0149 5.1815 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.3558 -1.5630 0.8348 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.2785 -1.4997 -0.0259 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8615 -0.3347 1.0810 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8763 -0.4401 2.0769 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.9593 -0.2226 -1.6039 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2573 0.2685 0.0844 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4156 1.0478 0.8414 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9092 0.5148 2.1160 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6110 0.7413 2.2052 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1998 -0.1971 1.1702 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3222 -0.0931 -0.0536 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1129 -0.1050 -1.3526 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2550 1.1964 -0.0026 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4768 0.0998 0.7873 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4082 -0.8770 0.9857 C 0 0 1 0 0 0 0 0 0 0 0 0 4.1119 -1.2234 -0.3115 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6067 -1.4581 -0.0387 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1687 -0.1263 0.4047 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1890 0.5630 1.2794 C 0 0 2 0 0 0 0 0 0 0 0 0 5.8278 1.5201 2.2596 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3408 -0.3373 1.9043 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4203 -0.2726 1.0035 O 0 0 0 0 0 0 0 0 0 0 0 0 8.3546 0.3664 0.1930 C 0 0 1 0 0 0 0 0 0 0 0 0 9.1664 1.3565 0.9593 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5498 1.5078 0.3526 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2599 0.1856 0.2001 C 0 0 1 0 0 0 0 0 0 0 0 0 10.2500 -0.9080 0.5044 C 0 0 2 0 0 0 0 0 0 0 0 0 10.8533 -2.2327 0.1592 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1579 -0.6741 -0.3315 O 0 0 0 0 0 0 0 0 0 0 0 0 11.6678 0.0106 -1.1304 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0840 -0.7392 -2.7620 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3100 -0.3889 -4.8367 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2480 0.2384 -6.1464 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5327 1.2609 -5.4825 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7916 2.2198 -4.2424 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8304 0.7379 -4.4155 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1436 1.0098 -2.2011 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2427 2.3862 -2.0413 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3284 1.9570 0.1106 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3060 0.7155 -3.0527 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1454 5.0953 -1.8015 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3251 5.2910 -3.2173 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5717 5.3055 -3.4624 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.4924 -2.8038 1.6858 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.8358 -4.0002 3.8650 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.0095 -4.0948 5.5072 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8496 -2.6471 6.1134 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3906 -1.3155 2.2370 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7641 -0.6660 -2.5026 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8522 2.0605 0.9820 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3512 1.0554 3.0047 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1389 -0.5599 2.2949 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8968 0.4726 3.2390 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7704 1.7952 1.9758 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1048 -1.2377 1.5933 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4534 -0.8738 -0.0902 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4874 -1.1168 -1.5077 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3889 0.1616 -2.1659 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9348 0.6360 -1.3330 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0359 -1.7995 1.4297 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7110 -2.1687 -0.6872 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0369 -0.4639 -1.0883 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0948 -1.7470 -0.9723 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7452 -2.1919 0.7771 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2569 0.4707 -0.5526 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5229 1.1920 0.6325 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2981 1.0189 3.1072 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4466 2.2329 1.7119 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9789 2.1248 2.6943 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8820 0.8313 -0.7192 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1776 1.1040 2.0186 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6789 2.3521 0.8432 H 0 0 0 0 0 0 0 0 0 0 0 0 11.1425 2.1420 1.0135 H 0 0 0 0 0 0 0 0 0 0 0 0 10.4021 2.0257 -0.6213 H 0 0 0 0 0 0 0 0 0 0 0 0 12.0926 0.0724 0.9112 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9362 -0.8718 1.5612 H 0 0 0 0 0 0 0 0 0 0 0 0 10.2247 -3.0358 0.5970 H 0 0 0 0 0 0 0 0 0 0 0 0 10.8326 -2.3529 -0.9606 H 0 0 0 0 0 0 0 0 0 0 0 0 11.9207 -2.3116 0.4366 H 0 0 0 0 0 0 0 0 0 0 0 0 10.9130 -0.3408 -1.6627 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2807 -1.0837 -3.2282 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 2 0 7 8 1 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 1 0 7 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 19 25 1 0 25 26 2 0 15 27 2 0 27 28 1 0 13 29 1 0 5 30 1 0 30 31 1 0 31 32 1 0 32 33 1 0 33 34 1 0 34 35 1 0 35 36 1 0 35 37 1 0 34 38 1 0 38 39 1 0 39 40 1 0 40 41 1 0 41 42 1 0 42 43 1 0 43 44 1 0 43 45 1 0 42 46 1 0 46 47 1 0 47 48 1 0 48 49 1 0 49 50 1 0 50 51 1 0 51 52 1 0 51 53 1 0 50 54 1 0 3 55 1 6 8 3 1 0 25 14 1 0 37 31 1 0 45 39 1 0 53 47 1 0 27 6 1 0 23 18 1 0 1 56 1 0 1 57 1 0 1 58 1 0 2 59 1 0 2 60 1 0 4 61 1 0 4 62 1 0 5 63 1 1 8 64 1 6 12 65 1 0 12 66 1 0 12 67 1 0 20 68 1 0 21 69 1 0 22 70 1 0 24 71 1 0 28 72 1 0 29 73 1 0 31 74 1 1 32 75 1 0 32 76 1 0 33 77 1 0 33 78 1 0 34 79 1 1 35 80 1 6 36 81 1 0 36 82 1 0 36 83 1 0 39 84 1 1 40 85 1 0 40 86 1 0 41 87 1 0 41 88 1 0 42 89 1 6 43 90 1 6 44 91 1 0 44 92 1 0 44 93 1 0 47 94 1 6 48 95 1 0 48 96 1 0 49 97 1 0 49 98 1 0 50 99 1 1 51100 1 1 52101 1 0 52102 1 0 52103 1 0 54104 1 0 55105 1 0 M END

Standard InCHIKey	VDCIZHNJZDCCAB-ORJPLPFJSA-N
Standard InCHI	InChI=1S/C40H50O15/c1-6-40(48)16-25(30-31(34(40)39(47)49-5)38(46)32-33(37(30)45)36(44)29-20(35(32)43)8-7-9-22(29)42)55-28-15-12-24(19(4)52-28)54-27-14-11-23(18(3)51-27)53-26-13-10-21(41)17(2)50-26/h7-9,17-19,21,23-28,34,41-42,45-46,48H,6,10-16H2,1-5H3/t17-,18-,19-,21-,23-,24-,25-,26-,27-,28-,34-,40+/m0/s1
SMILES	CC[C@]1(C[C@@H](c2c([C@H]1C(=O)OC)c(c1c(C(=O)c3c(cccc3O)C1=O)c2O)O)O[C@H]1CC[C@@H]([C@H](C)O1)O[C@H]1CC[C@@H]([C@H](C)O1)O[C@H]1CC[C@@H]([C@H](C)O1)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	770.31	Volume:	748.626 ? Van der Waals volume.
Dense:	1.029	LogP:	3.64 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.429 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.705 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	42.0
TPSA:	216.97 ? Topological Polar Surface Area.	H-Bond Acceptor:	15.0
H-Bond Donor:	5.0	Rings:	7.0
Heavy Atoms:	15.0

MedChem Properties

QED Drug-Likeness Score:	0.161	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.711	Fsp³:	0.625
MCE-18:	168.477 ? 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:	1
Colloidal aggregators:	0.686	Fluc inhibitor:	0.21 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.343 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.578 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.219	Promiscuous compounds:	0.943

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.495	MDCK Permeability:	-5.025
Pgp-inhibitor:	0.538	Pgp-substrate:	0.999
PAMPA:	1.0 ? 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):	0.079
20% Bioavailability (F20%):	0.17	30% Bioavailability (F30%):	0.92
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.992
Plasma Protein Binding (PPB):	93.854%	Volume Distribution (VD):	1.145
Fu:	8.346% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.565
BSEP inhibitor:	0.816

ADMET: Metabolism

CYP1A2-inhibitor:	1.0	CYP1A2-substrate:	0.002
CYP2C19-inhibitor:	0.688	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.076	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.066
CYP3A4-inhibitor:	0.987	CYP3A4-substrate:	0.919
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.048
HLM stability:	0.079 ? 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):

8.747

Half-life (T1/2):

4.376

ADMET: Toxicity

hERG Blockers:	0.189	hERG Blockers (10um):	0.585
Human Hepatotoxicity (H-HT):	0.986	Drug-induced Liver Injury (DILI):	1.0
AMES Toxicity:	0.999	Rat Oral Acute Toxicity:	0.987
Maximum Recommended Daily Dose:	0.999	Skin Sensitization:	1.0
Carcinogencity:	0.725	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.972
Drug-induced Neurotoxicity:	0.154	Ototoxicity:	0.993
Hematotoxicity:	0.974	Drug-induced Nephrotoxicity:	0.97
Genotoxicity:	0.998	RPMI-8226 Immunitoxicity:	0.917
A549 Cytotoxicity:	1.0	Hek293 Cytotoxicity:	0.994
BCF:	0.815 ? 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:	3.713 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.479 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.688 ? 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
NPO40642	Streptomyces sp. SCSIO 1666/17C4	Strain	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[29767975]

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	6

Activity Type	# Activity
Cell line	6

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
NPT400	Cell line	MDA-MB-435	Homo sapiens	IC50	=	2700.0	nM	PMID[29767975]
NPT397	Cell line	NCI-H460	Homo sapiens	IC50	=	10000.0	nM	PMID[29767975]
NPT82	Cell line	MDA-MB-231	Homo sapiens	IC50	=	4500.0	nM	PMID[29767975]
NPT393	Cell line	HCT-116	Homo sapiens	IC50	=	200.0	nM	PMID[29767975]
NPT65	Cell line	HepG2	Homo sapiens	IC50	=	1700.0	nM	PMID[29767975]
NPT2257	Cell line	MCF-10A	Homo sapiens	IC50	=	1400.0	nM	PMID[29767975]

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 NPC487395 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	15294
0.1-0.2	33633
0.2-0.3	849
0.3-0.4	53
0.4-0.5	10
0.5-0.6	12
0.6-0.7	5
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9136	High Similarity	NPC487383
0.7349	Intermediate Similarity	NPC603758
0.6556	Remote Similarity	NPC487384
0.6444	Remote Similarity	NPC487385
0.6444	Remote Similarity	NPC487387
0.6374	Remote Similarity	NPC487386
0.6	Remote Similarity	NPC487389
0.5978	Remote Similarity	NPC604442
0.5833	Remote Similarity	NPC487394
0.5824	Remote Similarity	NPC487388
0.5761	Remote Similarity	NPC487390
0.5631	Remote Similarity	NPC484443
0.5421	Remote Similarity	NPC611804
0.5263	Remote Similarity	NPC487391
0.5263	Remote Similarity	NPC487392
0.5213	Remote Similarity	NPC605190
0.5155	Remote Similarity	NPC487393
0.5122	Remote Similarity	NPC218870
0.505	Remote Similarity	NPC604609

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC487395 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4573
0.1-0.2	4531
0.2-0.3	16
0.3-0.4	28
0.4-0.5	0
0.5-0.6	2
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
0.5421	Remote Similarity	NPD8319	Approved
0.5421	Remote Similarity	NPD8320	Phase 3

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