NPASS Compound

Natural Product: NPC509449

Natural Product ID	NPC509449
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	5,7-dihydroxy-2-[4-[(2~{S},3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxyphenyl]-3-[(2~{S},3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-[[(2~{R},3~{R},4~{S},5~{R},6~{S})-3,4,5-trihydroxy-6-methyl-tetrahydropyran-2-yl]oxymethyl]tetrahydropyran-2-yl]oxy-chromen-4-one
IUPAC Name	5,7-dihydroxy-2-[4-[(2~{S},3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxyphenyl]-3-[(2~{S},3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-[[(2~{R},3~{R},4~{S},5~{R},6~{S})-3,4,5-trihydroxy-6-methyl-tetrahydropyran-2-yl]oxymethyl]tetrahydropyran-2-yl]oxy-chromen-4-one
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 93 98 0 0 0 0 0 0 0 0999 V2000 5.3050 1.5679 -3.9607 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3843 0.0869 -3.7485 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3348 -0.4387 -3.0109 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3229 0.2328 -1.7352 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2280 -0.1398 -1.0417 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1046 0.4827 -0.8581 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0907 1.8436 -0.2575 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7585 2.2068 -0.0903 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3326 2.3952 1.2111 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4619 1.3326 1.9826 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2052 0.4865 2.9460 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6882 -0.5445 2.8779 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5359 -0.9084 1.7576 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0427 -2.2386 1.7310 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9417 -2.6308 0.8107 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4579 -1.8142 -0.1758 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3695 -2.3330 -1.0324 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0856 -1.6519 -2.0608 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.2610 -1.1331 -1.4779 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9161 -0.3858 -2.4494 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.9893 0.4873 -1.8651 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6414 1.2126 -2.8507 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5131 -1.3744 -3.4635 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.4116 -0.7090 -4.2478 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3356 -1.9302 -4.2118 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.8504 -2.9052 -5.0763 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2969 -2.4625 -3.2771 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0807 -2.4437 -4.0135 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9777 -0.5154 -0.1725 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0310 -0.1137 0.8002 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7936 -1.3108 3.9753 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1412 -1.1632 5.0714 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3517 -2.0336 6.1482 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3589 -1.8460 7.3105 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2003 -2.6642 8.4146 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2950 -0.7939 7.4309 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4906 0.0440 6.3757 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4114 1.1072 6.4383 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7804 -0.1409 5.2160 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9566 0.6866 4.1554 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7924 1.6553 4.2151 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0998 3.6228 1.7805 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5050 4.7848 1.2571 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5307 3.5120 1.4568 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3979 3.9174 2.4387 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8793 2.0843 0.9650 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2643 2.1831 0.6874 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6108 -0.0965 -1.0356 C 0 0 2 0 0 0 0 0 0 0 0 0 6.3845 1.0860 -0.9470 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4014 -1.0939 -1.9008 C 0 0 1 0 0 0 0 0 0 0 0 0 5.6820 -2.2258 -2.1544 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7326 -0.2824 -3.1648 C 0 0 1 0 0 0 0 0 0 0 0 0 7.5145 -1.0048 -4.0519 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9083 2.1921 -3.2960 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2334 1.9097 -4.0168 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7138 1.7709 -4.9886 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3827 -0.4205 -4.7701 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2928 1.2835 -2.0454 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4411 0.4881 -1.8038 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4400 -0.1760 -0.1783 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5129 2.5359 -1.0702 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7007 2.8017 1.1790 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6717 -2.9290 2.4721 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2758 -3.6879 0.8708 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4848 -0.7364 -2.3103 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1578 0.2149 -2.9903 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5993 1.1316 -1.0470 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7497 -0.1709 -1.3573 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.5236 1.5493 -2.5453 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0090 -2.1912 -2.8820 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3747 -0.8556 -4.0321 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9139 -1.0817 -4.8099 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7483 -3.2276 -4.7899 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5382 -3.5242 -3.0250 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3075 -2.6457 -4.9634 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3419 0.1649 -0.9195 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7296 0.9100 0.7397 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0643 -2.8319 6.0522 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2453 -3.5572 8.3265 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8217 -0.6992 8.3647 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2912 1.0877 5.9509 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9094 3.6493 2.8384 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6368 4.8770 0.2774 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7481 4.1491 0.5499 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8370 3.1140 2.8603 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7012 1.3230 1.7143 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8230 1.7592 1.3602 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3899 -0.5267 -0.0368 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1240 0.9666 -0.2933 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3056 -1.3460 -1.3150 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2017 -3.0502 -2.2548 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3055 0.5944 -2.8345 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3120 -0.5042 -4.3867 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 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 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 20 23 1 0 23 24 1 0 23 25 1 0 25 26 1 0 25 27 1 0 27 28 1 0 16 29 1 0 29 30 2 0 12 31 1 0 31 32 1 0 32 33 2 0 33 34 1 0 34 35 1 0 34 36 2 0 36 37 1 0 37 38 1 0 37 39 2 0 39 40 1 0 40 41 2 0 9 42 1 0 42 43 1 0 42 44 1 0 44 45 1 0 44 46 1 0 46 47 1 0 4 48 1 0 48 49 1 0 48 50 1 0 50 51 1 0 50 52 1 0 52 53 1 0 52 2 1 0 46 7 1 0 40 11 1 0 30 13 1 0 39 32 1 0 27 18 1 0 1 54 1 0 1 55 1 0 1 56 1 0 2 57 1 6 4 58 1 6 6 59 1 0 6 60 1 0 7 61 1 6 9 62 1 6 14 63 1 0 15 64 1 0 18 65 1 6 20 66 1 6 21 67 1 0 21 68 1 0 22 69 1 0 23 70 1 1 24 71 1 0 25 72 1 6 26 73 1 0 27 74 1 1 28 75 1 0 29 76 1 0 30 77 1 0 33 78 1 0 35 79 1 0 36 80 1 0 38 81 1 0 42 82 1 1 43 83 1 0 44 84 1 6 45 85 1 0 46 86 1 1 47 87 1 0 48 88 1 1 49 89 1 0 50 90 1 1 51 91 1 0 52 92 1 1 53 93 1 0 M END

Standard InCHIKey	FYJOVKRHRUYSLY-XEQUTGBOSA-N
Standard InCHI	InChI=1S/C33H40O20/c1-10-19(37)23(41)26(44)31(48-10)47-9-17-21(39)25(43)28(46)33(52-17)53-30-22(40)18-14(36)6-12(35)7-15(18)50-29(30)11-2-4-13(5-3-11)49-32-27(45)24(42)20(38)16(8-34)51-32/h2-7,10,16-17,19-21,23-28,31-39,41-46H,8-9H2,1H3/t10-,16+,17+,19-,20+,21+,23-,24-,25-,26+,27+,28+,31+,32+,33-/m0/s1
SMILES	C[C@@H]1O[C@@H](OC[C@H]2O[C@@H](OC3=C(C4=CC=C(O[C@@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@H]5O)C=C4)OC4=CC(O)=CC(O)=C4C3=O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@H]1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	756.21	Volume:	682.698 ? Van der Waals volume.
Dense:	1.108	LogP:	0.137 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.999 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.983 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	36.0
TPSA:	328.35 ? Topological Polar Surface Area.	H-Bond Acceptor:	20.0
H-Bond Donor:	12.0	Rings:	6.0
Heavy Atoms:	20.0

MedChem Properties

QED Drug-Likeness Score:	0.099	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.291	Fsp³:	0.545
MCE-18:	150.706 ? 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:	0.612	Fluc inhibitor:	0.305 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.661 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.551 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.21	Promiscuous compounds:	0.539

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.928	MDCK Permeability:	-4.813
Pgp-inhibitor:	0.0	Pgp-substrate:	0.959
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):	0.894
20% Bioavailability (F20%):	0.036	30% Bioavailability (F30%):	0.998
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.001
Plasma Protein Binding (PPB):	79.425%	Volume Distribution (VD):	-0.137
Fu:	18.153% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.179
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	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:	0.997
HLM stability:	0.003 ? 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):

0.622

Half-life (T1/2):

5.949

ADMET: Toxicity

hERG Blockers:	0.004	hERG Blockers (10um):	0.043
Human Hepatotoxicity (H-HT):	0.664	Drug-induced Liver Injury (DILI):	0.987
AMES Toxicity:	0.928	Rat Oral Acute Toxicity:	0.002
Maximum Recommended Daily Dose:	0.004	Skin Sensitization:	0.998
Carcinogencity:	0.017	Eye Corrosion:	0.0
Eye Irritation:	0.046	Respiratory Toxicity:	0.001
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.992
Hematotoxicity:	0.069	Drug-induced Nephrotoxicity:	0.8
Genotoxicity:	0.581	RPMI-8226 Immunitoxicity:	0.225
A549 Cytotoxicity:	0.491	Hek293 Cytotoxicity:	0.291
BCF:	0.442 ? 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:	3.178 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.813 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.863 ? 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
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	DOI[10.1016/j.foodchem.2007.08.004]
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1016/j.phytochem.2007.01.008]
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota	n.a.	fruit	n.a.	PMID[17328933]
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO43130	Erodium spp.	Genus	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO51485	Geranium rotundifolium	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO47485	Geranium yemens	Genus	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO15336	Prunus avium	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO15336	Prunus avium	Species	Rosaceae	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

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

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 NPC509449 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	17332
0.1-0.2	27457
0.2-0.3	3916
0.3-0.4	596
0.4-0.5	273
0.5-0.6	73
0.6-0.7	98
0.7-0.8	1
0.8-0.85	7
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8256	Intermediate Similarity	NPC173582
0.8256	Intermediate Similarity	NPC265885
0.8256	Intermediate Similarity	NPC181465
0.8256	Intermediate Similarity	NPC215710
0.8256	Intermediate Similarity	NPC473438
0.8256	Intermediate Similarity	NPC253788
0.8	Intermediate Similarity	NPC473327
0.7955	Intermediate Similarity	NPC203259
0.7955	Intermediate Similarity	NPC33054
0.7955	Intermediate Similarity	NPC176740
0.7955	Intermediate Similarity	NPC471725
0.7955	Intermediate Similarity	NPC134532
0.7955	Intermediate Similarity	NPC156869
0.7955	Intermediate Similarity	NPC602582
0.7927	Intermediate Similarity	NPC64305
0.7841	Intermediate Similarity	NPC39834
0.7604	Intermediate Similarity	NPC189564
0.7529	Intermediate Similarity	NPC472459
0.7528	Intermediate Similarity	NPC187379
0.75	Intermediate Similarity	NPC203145
0.7474	Intermediate Similarity	NPC602448
0.7447	Intermediate Similarity	NPC476472
0.7447	Intermediate Similarity	NPC294815
0.7447	Intermediate Similarity	NPC16194
0.7347	Intermediate Similarity	NPC292019
0.7347	Intermediate Similarity	NPC202908
0.7263	Intermediate Similarity	NPC76831
0.7143	Intermediate Similarity	NPC471079
0.701	Intermediate Similarity	NPC287889
0.6981	Remote Similarity	NPC192539
0.6977	Remote Similarity	NPC77672
0.6977	Remote Similarity	NPC133671
0.6977	Remote Similarity	NPC135391
0.6977	Remote Similarity	NPC78263
0.6977	Remote Similarity	NPC250069
0.6947	Remote Similarity	NPC12013
0.6947	Remote Similarity	NPC11432
0.6947	Remote Similarity	NPC477613
0.6915	Remote Similarity	NPC186816
0.6882	Remote Similarity	NPC67326
0.6854	Remote Similarity	NPC60735
0.6854	Remote Similarity	NPC26230
0.6809	Remote Similarity	NPC65563
0.6809	Remote Similarity	NPC470949
0.6778	Remote Similarity	NPC120099
0.6765	Remote Similarity	NPC25523
0.6739	Remote Similarity	NPC116864
0.6739	Remote Similarity	NPC244776
0.6737	Remote Similarity	NPC473571
0.6737	Remote Similarity	NPC110941
0.6735	Remote Similarity	NPC89127
0.6705	Remote Similarity	NPC145038
0.6705	Remote Similarity	NPC56077
0.6705	Remote Similarity	NPC281131
0.6705	Remote Similarity	NPC253662
0.6705	Remote Similarity	NPC179950
0.6705	Remote Similarity	NPC88789
0.6705	Remote Similarity	NPC491374
0.6701	Remote Similarity	NPC122467
0.6667	Remote Similarity	NPC111929
0.6667	Remote Similarity	NPC292929
0.6667	Remote Similarity	NPC320283
0.6667	Remote Similarity	NPC221342
0.6667	Remote Similarity	NPC41121
0.6667	Remote Similarity	NPC476470
0.6591	Remote Similarity	NPC19388
0.6591	Remote Similarity	NPC240431
0.6591	Remote Similarity	NPC55786
0.6526	Remote Similarity	NPC163242
0.6526	Remote Similarity	NPC272068
0.6495	Remote Similarity	NPC488073
0.6495	Remote Similarity	NPC126784
0.6495	Remote Similarity	NPC241423
0.6484	Remote Similarity	NPC219904
0.6442	Remote Similarity	NPC480441
0.6421	Remote Similarity	NPC139320
0.6421	Remote Similarity	NPC609888
0.6413	Remote Similarity	NPC609478
0.6404	Remote Similarity	NPC289667
0.6404	Remote Similarity	NPC127546
0.6404	Remote Similarity	NPC57625
0.6404	Remote Similarity	NPC173637
0.6404	Remote Similarity	NPC317489
0.6404	Remote Similarity	NPC223424
0.6404	Remote Similarity	NPC600591
0.6374	Remote Similarity	NPC325555
0.6374	Remote Similarity	NPC226304
0.6346	Remote Similarity	NPC173837
0.6327	Remote Similarity	NPC153755
0.6311	Remote Similarity	NPC89052
0.6292	Remote Similarity	NPC135599
0.6292	Remote Similarity	NPC73855
0.6292	Remote Similarity	NPC113968
0.6292	Remote Similarity	NPC328940
0.6292	Remote Similarity	NPC277174
0.6292	Remote Similarity	NPC606877
0.6289	Remote Similarity	NPC155877
0.6289	Remote Similarity	NPC605592
0.6286	Remote Similarity	NPC303694
0.6277	Remote Similarity	NPC203050
0.6277	Remote Similarity	NPC225434
0.625	Remote Similarity	NPC288084
0.6226	Remote Similarity	NPC277532
0.6224	Remote Similarity	NPC129264
0.6222	Remote Similarity	NPC143851
0.619	Remote Similarity	NPC48984
0.6186	Remote Similarity	NPC470405
0.6186	Remote Similarity	NPC471748
0.617	Remote Similarity	NPC116458
0.617	Remote Similarity	NPC246943
0.6154	Remote Similarity	NPC265530
0.6132	Remote Similarity	NPC470712
0.6105	Remote Similarity	NPC170052
0.6105	Remote Similarity	NPC476215
0.6105	Remote Similarity	NPC135846
0.61	Remote Similarity	NPC470443
0.6082	Remote Similarity	NPC29958
0.6078	Remote Similarity	NPC85751
0.6078	Remote Similarity	NPC471669
0.6078	Remote Similarity	NPC19240
0.604	Remote Similarity	NPC270448
0.6038	Remote Similarity	NPC219043
0.6	Remote Similarity	NPC223747
0.6	Remote Similarity	NPC67037
0.6	Remote Similarity	NPC470125
0.6	Remote Similarity	NPC255615
0.6	Remote Similarity	NPC480445
0.5982	Remote Similarity	NPC241781
0.5979	Remote Similarity	NPC251417
0.596	Remote Similarity	NPC304741
0.5946	Remote Similarity	NPC162394
0.5946	Remote Similarity	NPC474522
0.5922	Remote Similarity	NPC473073
0.5922	Remote Similarity	NPC220173
0.5905	Remote Similarity	NPC214621
0.5905	Remote Similarity	NPC34267
0.5889	Remote Similarity	NPC34531
0.5882	Remote Similarity	NPC37668
0.5876	Remote Similarity	NPC254855
0.5876	Remote Similarity	NPC94610
0.5876	Remote Similarity	NPC95866
0.5856	Remote Similarity	NPC470713
0.5851	Remote Similarity	NPC21100
0.5833	Remote Similarity	NPC605784
0.5825	Remote Similarity	NPC142142
0.5812	Remote Similarity	NPC473554
0.581	Remote Similarity	NPC223426
0.581	Remote Similarity	NPC135358
0.5806	Remote Similarity	NPC297987
0.5804	Remote Similarity	NPC156785
0.58	Remote Similarity	NPC22062
0.58	Remote Similarity	NPC473634
0.58	Remote Similarity	NPC138811
0.5789	Remote Similarity	NPC175107
0.5769	Remote Similarity	NPC470447
0.5755	Remote Similarity	NPC14187
0.5755	Remote Similarity	NPC81042
0.5752	Remote Similarity	NPC480444
0.5743	Remote Similarity	NPC204693
0.5743	Remote Similarity	NPC255157
0.5743	Remote Similarity	NPC259896
0.5741	Remote Similarity	NPC477895
0.5729	Remote Similarity	NPC224530
0.5728	Remote Similarity	NPC32641
0.5728	Remote Similarity	NPC256188
0.5728	Remote Similarity	NPC35119
0.5726	Remote Similarity	NPC487499
0.5714	Remote Similarity	NPC470449
0.57	Remote Similarity	NPC67105
0.5686	Remote Similarity	NPC488074
0.567	Remote Similarity	NPC136761
0.5625	Remote Similarity	NPC488734
0.5625	Remote Similarity	NPC159579
0.5625	Remote Similarity	NPC191306
0.5625	Remote Similarity	NPC488735
0.5625	Remote Similarity	NPC488739
0.5625	Remote Similarity	NPC488732
0.5625	Remote Similarity	NPC488738
0.562	Remote Similarity	NPC249560
0.5604	Remote Similarity	NPC54802
0.5604	Remote Similarity	NPC197304
0.5579	Remote Similarity	NPC46420
0.5579	Remote Similarity	NPC488080
0.5579	Remote Similarity	NPC169977
0.5577	Remote Similarity	NPC209296
0.5566	Remote Similarity	NPC470445
0.5545	Remote Similarity	NPC44931
0.5545	Remote Similarity	NPC217520
0.5545	Remote Similarity	NPC275454
0.5545	Remote Similarity	NPC227508
0.5534	Remote Similarity	NPC296018
0.5534	Remote Similarity	NPC240306
0.5534	Remote Similarity	NPC64425
0.5532	Remote Similarity	NPC249281
0.5521	Remote Similarity	NPC216496
0.5514	Remote Similarity	NPC470446
0.549	Remote Similarity	NPC210073
0.5474	Remote Similarity	NPC8573
0.5474	Remote Similarity	NPC156457
0.5474	Remote Similarity	NPC136042

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC509449 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4991
0.1-0.2	4079
0.2-0.3	67
0.3-0.4	6
0.4-0.5	1
0.5-0.6	3
0.6-0.7	2
0.7-0.8	1
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
0.7955	Intermediate Similarity	NPD6797	Phase 2
0.6471	Remote Similarity	NPD7808	Phase 3
0.64	Remote Similarity	NPD7251	Phase 2
0.5577	Remote Similarity	NPD7054	Phase 4
0.5377	Remote Similarity	NPD7804	Clinical (unspecified phase)
0.5135	Remote Similarity	NPD7472	Pre-clinical

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