NPASS Compound

Natural Product: NPC587934

Natural Product ID	NPC587934
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	2-(3,4-dihydroxy-5-methoxy-phenyl)-5-hydroxy-7-[(2~{S},3~{R},4~{S},5~{R},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-3-[(2~{S},3~{R},4~{S},5~{R},6~{R})-3,4,5-trihydroxy-6-[[(2~{R},3~{R},4~{S},5~{R},6~{R})-3,4,5-trihydroxy-6-methyl-tetrahydropyran-2-yl]oxymethyl]tetrahydropyran-2-yl]oxy-chromen-4-one
IUPAC Name	2-(3,4-dihydroxy-5-methoxy-phenyl)-5-hydroxy-7-[(2~{S},3~{R},4~{S},5~{R},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-3-[(2~{S},3~{R},4~{S},5~{R},6~{R})-3,4,5-trihydroxy-6-[[(2~{R},3~{R},4~{S},5~{R},6~{R})-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] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-O-glycosides

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 3.1387 -6.2673 -2.6959 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9049 -6.7500 -2.2439 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0321 -5.9854 -1.5104 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2587 -4.6870 -1.1409 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3823 -3.9066 -0.3994 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8012 -2.5683 -0.0157 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0723 -1.6130 0.4003 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4642 -1.7854 0.4819 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2274 -1.2678 -0.6293 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.0116 -0.1955 -0.1512 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7240 0.3075 -1.2437 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0454 1.7419 -1.1966 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7734 2.2673 -0.2052 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0884 1.9984 -0.0223 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.7673 3.1991 -0.2314 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6743 3.5068 0.7561 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.3547 4.8009 0.3941 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8800 3.7203 2.0279 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.7104 4.4134 1.6764 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4334 2.3412 2.4543 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.2151 2.4068 3.1727 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3317 1.3943 1.3184 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.4780 0.5980 1.3050 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8226 -0.6166 -1.5917 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.5457 -1.1150 -0.4889 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1590 -1.8815 -2.1631 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1012 -2.9267 -2.2462 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9414 -2.2972 -1.3955 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0887 -2.8846 -2.3873 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4467 -0.3637 0.7560 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3665 0.5106 1.1438 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7854 -0.1469 0.6706 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2506 1.1102 1.0325 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3658 2.0797 1.4611 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6272 1.3097 0.9329 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4687 0.3191 0.5021 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8231 0.5105 0.4005 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5602 1.6607 0.7101 C 0 0 2 0 0 0 0 0 0 0 0 0 6.9977 2.1757 -0.5263 O 0 0 0 0 0 0 0 0 0 0 0 0 7.8074 3.2752 -0.3977 C 0 0 1 0 0 0 0 0 0 0 0 0 7.1058 4.4678 0.1755 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0393 4.7956 -0.6868 O 0 0 0 0 0 0 0 0 0 0 0 0 9.0895 2.9516 0.3409 C 0 0 2 0 0 0 0 0 0 0 0 0 10.2220 3.0666 -0.4678 O 0 0 0 0 0 0 0 0 0 0 0 0 9.0365 1.4908 0.8075 C 0 0 2 0 0 0 0 0 0 0 0 0 9.0474 0.6620 -0.3097 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7418 1.2993 1.5833 C 0 0 1 0 0 0 0 0 0 0 0 0 7.8226 2.1352 2.7085 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9828 -0.9183 0.1500 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6061 -1.1555 0.2371 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1164 -2.3141 -0.0885 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7831 -4.4879 -0.0182 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0401 -5.8022 -0.3788 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2438 -6.3771 0.0230 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1689 -6.5678 -1.1128 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4311 -7.8910 -1.4743 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8688 -7.1044 -2.8870 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0726 -5.7503 -3.6967 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6525 -5.5739 -2.0211 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2142 -4.2502 -1.4686 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5130 -0.7597 -1.3517 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9676 0.2041 -2.1218 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6070 1.9853 -2.1771 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0810 2.3646 -1.3735 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4554 1.3283 -0.8134 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4453 2.6990 0.9227 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7145 5.4666 -0.2177 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2762 4.6200 -0.2218 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6726 5.3943 1.2845 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4507 4.2214 2.8084 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9656 4.1069 2.2525 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1879 1.9778 3.1992 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2134 1.6927 3.8516 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4832 0.6980 1.5607 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6869 0.2538 2.2101 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5042 -0.1845 -2.3159 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9075 -1.2407 0.2614 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8747 -1.6201 -3.1955 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8764 -3.6158 -1.5517 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2604 -3.1433 -0.7382 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3280 -3.8318 -2.4857 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6554 2.6611 2.2490 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0165 2.2919 1.2106 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9801 2.4439 1.2352 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1113 3.5651 -1.4424 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6922 4.3429 1.1756 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8094 5.3364 0.2346 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5803 5.6212 -0.3858 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2452 3.5976 1.2246 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9269 3.0243 -1.4149 H 0 0 0 0 0 0 0 0 0 0 0 0 9.8905 1.3193 1.4750 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5688 -0.1831 -0.1300 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7334 0.2548 1.9364 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7049 2.1007 3.1275 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5905 -1.7335 -0.1944 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5354 -3.9609 0.5958 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0548 -5.7944 0.2524 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2315 -8.5688 -1.0662 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 1 0 6 7 2 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 1 0 15 16 1 0 16 17 1 0 16 18 1 0 18 19 1 0 18 20 1 0 20 21 1 0 20 22 1 0 22 23 1 0 11 24 1 0 24 25 1 0 24 26 1 0 26 27 1 0 26 28 1 0 28 29 1 0 7 30 1 0 30 31 2 0 30 32 1 0 32 33 2 0 33 34 1 0 33 35 1 0 35 36 2 0 36 37 1 0 37 38 1 0 38 39 1 0 39 40 1 0 40 41 1 0 41 42 1 0 40 43 1 0 43 44 1 0 43 45 1 0 45 46 1 0 45 47 1 0 47 48 1 0 36 49 1 0 49 50 2 0 50 51 1 0 5 52 2 0 52 53 1 0 53 54 1 0 53 55 2 0 55 56 1 0 55 3 1 0 51 6 1 0 28 9 1 0 50 32 1 0 22 14 1 0 47 38 1 0 1 57 1 0 1 58 1 0 1 59 1 0 4 60 1 0 9 61 1 6 11 62 1 6 12 63 1 0 12 64 1 0 14 65 1 6 16 66 1 1 17 67 1 0 17 68 1 0 17 69 1 0 18 70 1 1 19 71 1 0 20 72 1 1 21 73 1 0 22 74 1 1 23 75 1 0 24 76 1 6 25 77 1 0 26 78 1 6 27 79 1 0 28 80 1 1 29 81 1 0 34 82 1 0 35 83 1 0 38 84 1 1 40 85 1 6 41 86 1 0 41 87 1 0 42 88 1 0 43 89 1 1 44 90 1 0 45 91 1 1 46 92 1 0 47 93 1 1 48 94 1 0 49 95 1 0 52 96 1 0 54 97 1 0 56 98 1 0 M END

Standard InCHIKey	OKKLDYKZUSTYOZ-CIKBWTFPSA-N
Standard InCHI	InChI=1S/C34H42O22/c1-9-19(38)24(43)27(46)32(51-9)50-8-17-22(41)26(45)29(48)34(55-17)56-31-23(42)18-12(36)5-11(52-33-28(47)25(44)21(40)16(7-35)54-33)6-14(18)53-30(31)10-3-13(37)20(39)15(4-10)49-2/h3-6,9,16-17,19,21-22,24-29,32-41,43-48H,7-8H2,1-2H3/t9-,16+,17-,19+,21+,22+,24+,25+,26+,27-,28-,29-,32-,33-,34+/m1/s1
SMILES	COC1=CC(C2=C(O[C@@H]3O[C@H](CO[C@@H]4O[C@H](C)[C@H](O)[C@H](O)[C@H]4O)[C@H](O)[C@H](O)[C@H]3O)C(=O)C3=C(O)C=C(O[C@@H]4O[C@@H](CO)[C@H](O)[C@H](O)[C@H]4O)C=C3O2)=CC(O)=C1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	802.22	Volume:	717.575 ? Van der Waals volume.
Dense:	1.118	LogP:	-0.415 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.853 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.412 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	10.0	Rigid Bonds:	36.0
TPSA:	357.81 ? Topological Polar Surface Area.	H-Bond Acceptor:	22.0
H-Bond Donor:	13.0	Rings:	6.0
Heavy Atoms:	22.0

MedChem Properties

QED Drug-Likeness Score:	0.086	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.478	Fsp³:	0.559
MCE-18:	156.906 ? 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:	1	PAINS Alert:	1
Colloidal aggregators:	0.636	Fluc inhibitor:	0.152 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.706 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.638 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.131	Promiscuous compounds:	0.586

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.765	MDCK Permeability:	-5.145
Pgp-inhibitor:	0.0	Pgp-substrate:	0.905
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):	1.0
20% Bioavailability (F20%):	0.958	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.195
Plasma Protein Binding (PPB):	79.094%	Volume Distribution (VD):	-0.119
Fu:	20.282% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.344
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:	0.005
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.132
HLM stability:	0.002 ? 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):

0.895

Half-life (T1/2):

3.947

ADMET: Toxicity

hERG Blockers:	0.002	hERG Blockers (10um):	0.037
Human Hepatotoxicity (H-HT):	0.778	Drug-induced Liver Injury (DILI):	0.996
AMES Toxicity:	0.996	Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.002	Skin Sensitization:	1.0
Carcinogencity:	0.033	Eye Corrosion:	0.0
Eye Irritation:	0.024	Respiratory Toxicity:	0.002
Drug-induced Neurotoxicity:	0.001	Ototoxicity:	0.992
Hematotoxicity:	0.606	Drug-induced Nephrotoxicity:	0.917
Genotoxicity:	0.945	RPMI-8226 Immunitoxicity:	0.331
A549 Cytotoxicity:	0.995	Hek293 Cytotoxicity:	0.632
BCF:	0.288 ? 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:	2.893 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.681 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.673 ? 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
NPO49435	Limnanthes douglasii	Species	Limnanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28111	Lathyrus aphaca	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28111	Lathyrus aphaca	Species	Fabaceae	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 NPC587934 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	23346
0.1-0.2	22499
0.2-0.3	3030
0.3-0.4	509
0.4-0.5	286
0.5-0.6	130
0.6-0.7	48
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	Natural Product ID
0.7263	Intermediate Similarity	NPC186816
0.7255	Intermediate Similarity	NPC480441
0.6939	Remote Similarity	NPC470443
0.6923	Remote Similarity	NPC25523
0.6882	Remote Similarity	NPC605784
0.6633	Remote Similarity	NPC210073
0.6538	Remote Similarity	NPC14187
0.6535	Remote Similarity	NPC209296
0.6531	Remote Similarity	NPC275454
0.6531	Remote Similarity	NPC67105
0.6531	Remote Similarity	NPC227508
0.6526	Remote Similarity	NPC116458
0.6526	Remote Similarity	NPC246943
0.6522	Remote Similarity	NPC158674
0.6522	Remote Similarity	NPC136042
0.6495	Remote Similarity	NPC251417
0.6465	Remote Similarity	NPC22062
0.6465	Remote Similarity	NPC473634
0.6465	Remote Similarity	NPC138811
0.6452	Remote Similarity	NPC84362
0.6452	Remote Similarity	NPC271692
0.6408	Remote Similarity	NPC476472
0.6408	Remote Similarity	NPC294815
0.6408	Remote Similarity	NPC16194
0.6364	Remote Similarity	NPC39834
0.6337	Remote Similarity	NPC488073
0.6337	Remote Similarity	NPC126784
0.6337	Remote Similarity	NPC241423
0.63	Remote Similarity	NPC203259
0.63	Remote Similarity	NPC33054
0.63	Remote Similarity	NPC176740
0.63	Remote Similarity	NPC471725
0.63	Remote Similarity	NPC134532
0.63	Remote Similarity	NPC156869
0.63	Remote Similarity	NPC602582
0.6239	Remote Similarity	NPC277532
0.6237	Remote Similarity	NPC289667
0.6214	Remote Similarity	NPC473327
0.62	Remote Similarity	NPC44931
0.617	Remote Similarity	NPC297987
0.6154	Remote Similarity	NPC142142
0.6146	Remote Similarity	NPC611303
0.6105	Remote Similarity	NPC46420
0.6095	Remote Similarity	NPC473073
0.604	Remote Similarity	NPC173582
0.604	Remote Similarity	NPC265885
0.604	Remote Similarity	NPC181465
0.604	Remote Similarity	NPC215710
0.604	Remote Similarity	NPC473438
0.604	Remote Similarity	NPC253788
0.5922	Remote Similarity	NPC473571
0.5922	Remote Similarity	NPC110941
0.5909	Remote Similarity	NPC292019
0.5909	Remote Similarity	NPC202908
0.5905	Remote Similarity	NPC32641
0.5905	Remote Similarity	NPC256188
0.5905	Remote Similarity	NPC35119
0.5895	Remote Similarity	NPC249281
0.5865	Remote Similarity	NPC240306
0.5833	Remote Similarity	NPC135358
0.5825	Remote Similarity	NPC65563
0.5825	Remote Similarity	NPC470949
0.58	Remote Similarity	NPC276377
0.5739	Remote Similarity	NPC198199
0.5727	Remote Similarity	NPC121703
0.5701	Remote Similarity	NPC486577
0.5686	Remote Similarity	NPC480463
0.5678	Remote Similarity	NPC192539
0.5676	Remote Similarity	NPC189564
0.5673	Remote Similarity	NPC150164
0.5664	Remote Similarity	NPC311850
0.5631	Remote Similarity	NPC480466
0.5607	Remote Similarity	NPC606657
0.5593	Remote Similarity	NPC120952
0.5586	Remote Similarity	NPC203145
0.5566	Remote Similarity	NPC64425
0.5556	Remote Similarity	NPC325555
0.5556	Remote Similarity	NPC226304
0.5545	Remote Similarity	NPC311830
0.5517	Remote Similarity	NPC68592
0.5514	Remote Similarity	NPC65711
0.551	Remote Similarity	NPC277205
0.551	Remote Similarity	NPC37919
0.551	Remote Similarity	NPC189142
0.551	Remote Similarity	NPC77660
0.55	Remote Similarity	NPC488071
0.5481	Remote Similarity	NPC609888
0.5472	Remote Similarity	NPC204693
0.5463	Remote Similarity	NPC473623
0.5455	Remote Similarity	NPC58382
0.5446	Remote Similarity	NPC22832
0.5429	Remote Similarity	NPC67326
0.5421	Remote Similarity	NPC488074
0.5413	Remote Similarity	NPC488089
0.5405	Remote Similarity	NPC602448
0.5377	Remote Similarity	NPC479405
0.5377	Remote Similarity	NPC303913
0.5354	Remote Similarity	NPC95090
0.5354	Remote Similarity	NPC27408
0.534	Remote Similarity	NPC203050
0.534	Remote Similarity	NPC488072
0.534	Remote Similarity	NPC225434
0.534	Remote Similarity	NPC601586
0.5333	Remote Similarity	NPC209550
0.5327	Remote Similarity	NPC479404
0.5321	Remote Similarity	NPC72016
0.531	Remote Similarity	NPC89052
0.531	Remote Similarity	NPC11468
0.5306	Remote Similarity	NPC473043
0.53	Remote Similarity	NPC27640
0.53	Remote Similarity	NPC349108
0.53	Remote Similarity	NPC603655
0.5294	Remote Similarity	NPC243930
0.5294	Remote Similarity	NPC486578
0.5294	Remote Similarity	NPC601144
0.5278	Remote Similarity	NPC475366
0.5278	Remote Similarity	NPC153755
0.5268	Remote Similarity	NPC470446
0.5253	Remote Similarity	NPC19388
0.5253	Remote Similarity	NPC261866
0.5253	Remote Similarity	NPC240431
0.5253	Remote Similarity	NPC55786
0.5253	Remote Similarity	NPC19709
0.5253	Remote Similarity	NPC238376
0.525	Remote Similarity	NPC488078
0.5248	Remote Similarity	NPC42773
0.5248	Remote Similarity	NPC472459
0.5248	Remote Similarity	NPC59534
0.5248	Remote Similarity	NPC45522
0.5248	Remote Similarity	NPC599850
0.5246	Remote Similarity	NPC262222
0.5243	Remote Similarity	NPC607707
0.5229	Remote Similarity	NPC479403
0.5225	Remote Similarity	NPC195257
0.5225	Remote Similarity	NPC475382
0.5217	Remote Similarity	NPC173837
0.521	Remote Similarity	NPC298666
0.5207	Remote Similarity	NPC138990
0.52	Remote Similarity	NPC145038
0.52	Remote Similarity	NPC56077
0.52	Remote Similarity	NPC281131
0.52	Remote Similarity	NPC253662
0.52	Remote Similarity	NPC179950
0.52	Remote Similarity	NPC88789
0.52	Remote Similarity	NPC491374
0.5196	Remote Similarity	NPC285197
0.5189	Remote Similarity	NPC471079
0.5185	Remote Similarity	NPC115674
0.5182	Remote Similarity	NPC122467
0.5182	Remote Similarity	NPC229409
0.5179	Remote Similarity	NPC101636
0.5179	Remote Similarity	NPC470445
0.5164	Remote Similarity	NPC175429
0.5149	Remote Similarity	NPC24043
0.5146	Remote Similarity	NPC101026
0.5146	Remote Similarity	NPC120099
0.5146	Remote Similarity	NPC488077
0.5143	Remote Similarity	NPC116864
0.5143	Remote Similarity	NPC244776
0.5138	Remote Similarity	NPC46202
0.5135	Remote Similarity	NPC5319
0.5126	Remote Similarity	NPC295625
0.5124	Remote Similarity	NPC470720
0.5124	Remote Similarity	NPC488079
0.51	Remote Similarity	NPC39360
0.51	Remote Similarity	NPC29763
0.51	Remote Similarity	NPC210003
0.5096	Remote Similarity	NPC223747
0.5093	Remote Similarity	NPC102028
0.5089	Remote Similarity	NPC89127
0.5088	Remote Similarity	NPC244875
0.5085	Remote Similarity	NPC488083
0.505	Remote Similarity	NPC64305
0.505	Remote Similarity	NPC323593
0.505	Remote Similarity	NPC203500
0.5048	Remote Similarity	NPC355481
0.5047	Remote Similarity	NPC187379
0.5043	Remote Similarity	NPC473644
0.5041	Remote Similarity	NPC470719
0.5041	Remote Similarity	NPC470717

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC587934 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5885
0.1-0.2	3208
0.2-0.3	46
0.3-0.4	5
0.4-0.5	0
0.5-0.6	2
0.6-0.7	3
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
0.7245	Intermediate Similarity	NPD7251	Phase 2
0.6796	Remote Similarity	NPD7808	Phase 3
0.6535	Remote Similarity	NPD7054	Phase 4
0.63	Remote Similarity	NPD6797	Phase 2
0.531	Remote Similarity	NPD7472	Pre-clinical
0.5135	Remote Similarity	NPD7804	Clinical (unspecified phase)

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