NPASS Compound

Natural Product: NPC306746

Natural Product ID	NPC306746
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3,6-Beta,23-Trihydroxyolean-12-En-28-Oic Acid 28-O-Beta-D-Glucopyranoside
IUPAC Name	[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] (4aS,6aR,6aS,6bR,8R,8aR,9R,10S,12aR,14bS)-8,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1910835
PubChem CID	54671990
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

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 104109 0 0 0 0 0 0 0 0999 V2000 2.6189 -2.3554 4.1629 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7139 -2.1411 2.6361 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4114 -3.3808 2.1153 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4668 -0.8812 2.4028 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5866 0.2104 1.8584 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9510 -0.2460 0.5278 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3900 0.9401 -0.1522 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0217 0.7957 -0.7404 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9153 0.2456 0.2546 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1772 1.3417 1.2758 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4184 -1.0040 0.8975 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2865 -1.8063 1.4870 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7549 -1.6055 1.5894 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1666 -0.4576 0.7450 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.6500 -0.3989 0.4295 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2121 -1.6073 -0.2112 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3442 -0.2377 1.7804 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0840 1.0532 1.9247 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0462 1.1451 0.7664 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.2102 1.4116 -0.4623 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.0072 0.9861 -1.6504 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1009 2.9446 -0.5424 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3665 3.5151 -0.6566 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8418 0.8818 -0.3430 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1176 0.8625 -1.6634 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6413 0.8586 -1.3409 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2497 -0.2179 -0.3789 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9094 -1.4483 -1.1915 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3867 -0.2006 -2.4684 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6911 -0.0835 0.6474 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0469 -1.3649 0.8715 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3153 -2.0764 2.1503 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1149 -0.7087 -0.3149 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0892 -1.8856 -0.7201 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1384 0.1323 -0.6105 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2707 -0.2454 -1.4046 C 0 0 1 0 0 0 0 0 0 0 0 0 5.3067 0.7123 -2.5771 C 0 0 1 0 0 0 0 0 0 0 0 0 6.1598 1.9224 -2.2380 C 0 0 2 0 0 0 0 0 0 0 0 0 7.5772 1.4511 -2.0586 C 0 0 1 0 0 0 0 0 0 0 0 0 7.5462 0.1253 -1.3518 C 0 0 1 0 0 0 0 0 0 0 0 0 8.7287 0.0316 -0.4327 C 0 0 0 0 0 0 0 0 0 0 0 0 9.9371 0.1910 -1.1257 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3891 -0.0422 -0.5940 O 0 0 0 0 0 0 0 0 0 0 0 0 8.1417 1.2614 -3.3121 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6328 2.4311 -1.0313 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7199 0.0834 -3.7456 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6369 -2.7132 4.4651 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4009 -1.4179 4.6726 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8995 -3.1731 4.3772 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7991 -3.7733 1.2532 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4461 -3.1896 1.8294 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4084 -4.2101 2.8510 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9154 -0.4885 3.3438 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3233 -1.1102 1.7364 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8160 0.4698 2.5870 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2129 1.0938 1.6350 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4827 1.8278 0.5154 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0431 1.2479 -1.0382 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3069 1.8466 -1.0023 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1082 0.2866 -1.7015 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3183 0.9653 2.2998 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9872 2.0461 0.9345 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3010 2.0446 1.3739 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9368 -2.7401 1.9703 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3189 -2.5419 1.4001 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9346 -1.4192 2.6929 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0606 0.4387 1.4411 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9156 -2.1774 0.4714 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8371 -1.4112 -1.1082 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4881 -2.3832 -0.5273 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6335 -0.2976 2.6379 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0771 -1.0532 1.9695 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6939 0.9802 2.8464 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4379 1.9358 2.0233 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8032 1.9013 0.9641 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6656 0.1035 -1.3967 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4572 0.8616 -2.5798 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7672 1.7995 -1.8554 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5237 3.2621 -1.4109 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6373 3.3566 0.3636 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5391 3.8534 -1.5666 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2674 1.6472 0.2701 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3492 1.8036 -2.2024 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1216 0.6748 -2.3289 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3625 1.8746 -1.0553 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4460 -1.4556 -2.1852 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8349 -1.4893 -1.4697 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1285 -2.4007 -0.7244 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3929 -0.0350 -3.4260 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4437 -0.1457 1.2881 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1991 -2.1437 0.0499 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6985 -1.5795 2.9390 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9886 -3.1538 2.0280 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1921 -1.2969 -1.7334 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2842 1.0988 -2.7713 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0437 2.6743 -3.0333 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2019 2.1880 -1.4911 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5955 -0.7416 -2.0430 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6951 -0.9669 0.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6722 0.8514 0.3121 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9368 -0.2815 -1.9821 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7736 1.9572 -3.5785 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3648 2.8799 -0.5620 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1526 0.6799 -4.3911 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 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 1 9 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 6 15 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 6 20 22 1 0 22 23 1 0 20 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 6 25 29 1 0 19 30 1 0 11 31 1 0 31 32 1 0 6 33 1 6 33 34 2 0 33 35 1 0 35 36 1 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 39 44 1 0 38 45 1 0 37 46 1 0 32 2 1 0 43 36 1 0 31 6 1 0 27 9 1 0 27 14 1 0 24 15 1 0 1 47 1 0 1 48 1 0 1 49 1 0 3 50 1 0 3 51 1 0 3 52 1 0 4 53 1 0 4 54 1 0 5 55 1 0 5 56 1 0 7 57 1 0 7 58 1 0 8 59 1 0 8 60 1 0 10 61 1 0 10 62 1 0 10 63 1 0 12 64 1 0 13 65 1 0 13 66 1 0 14 67 1 1 16 68 1 0 16 69 1 0 16 70 1 0 17 71 1 0 17 72 1 0 18 73 1 0 18 74 1 0 19 75 1 1 21 76 1 0 21 77 1 0 21 78 1 0 22 79 1 0 22 80 1 0 23 81 1 0 24 82 1 1 25 83 1 6 26 84 1 0 26 85 1 0 28 86 1 0 28 87 1 0 28 88 1 0 29 89 1 0 30 90 1 0 31 91 1 6 32 92 1 0 32 93 1 0 36 94 1 6 37 95 1 6 38 96 1 6 39 97 1 1 40 98 1 6 41 99 1 0 41100 1 0 42101 1 0 44102 1 0 45103 1 0 46104 1 0 M END

Standard InCHIKey	ACQGRYACYVKOBB-ONXNPAKPSA-N
Standard InCHI	InChI=1S/C36H58O10/c1-31(2)11-13-36(30(44)46-29-27(43)26(42)25(41)22(17-37)45-29)14-12-34(5)19(20(36)15-31)7-8-23-32(3)10-9-24(40)33(4,18-38)28(32)21(39)16-35(23,34)6/h7,20-29,37-43H,8-18H2,1-6H3/t20-,21+,22+,23+,24-,25+,26-,27+,28+,29-,32+,33+,34+,35+,36-/m0/s1
SMILES	CC1(C)CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@@H]([C@@](C)(CO)[C@@H]5[C@@H](C[C@@]34C)O)O)[C@@H]2C1)C(=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	650.4	Volume:	662.503 ? Van der Waals volume.
Dense:	0.982	LogP:	2.421 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.672 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.108 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	33.0
TPSA:	177.14 ? Topological Polar Surface Area.	H-Bond Acceptor:	10.0
H-Bond Donor:	7.0	Rings:	6.0
Heavy Atoms:	10.0

MedChem Properties

QED Drug-Likeness Score:	0.177	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.515	Fsp³:	0.917
MCE-18:	130.783 ? 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:	0.863	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.028 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.166	Promiscuous compounds:	0.108

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.962	MDCK Permeability:	-5.208
Pgp-inhibitor:	0.004	Pgp-substrate:	0.023
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):	0.31
20% Bioavailability (F20%):	0.983	30% Bioavailability (F30%):	0.993
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.708	MRP1:	0.13
Plasma Protein Binding (PPB):	74.223%	Volume Distribution (VD):	-0.37
Fu:	20.67% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.946	BCRP inhibitor:	0.023
BSEP inhibitor:	0.28

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.024	CYP2C19-substrate:	0.12
CYP2C9-inhibitor:	0.001	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.001
CYP3A4-inhibitor:	0.054	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.787
HLM stability:	0.148 ? 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):

1.463

Half-life (T1/2):

2.477

ADMET: Toxicity

hERG Blockers:	0.012	hERG Blockers (10um):	0.031
Human Hepatotoxicity (H-HT):	0.691	Drug-induced Liver Injury (DILI):	0.314
AMES Toxicity:	0.741	Rat Oral Acute Toxicity:	0.075
Maximum Recommended Daily Dose:	0.062	Skin Sensitization:	1.0
Carcinogencity:	0.567	Eye Corrosion:	0.0
Eye Irritation:	0.004	Respiratory Toxicity:	0.062
Drug-induced Neurotoxicity:	0.006	Ototoxicity:	0.982
Hematotoxicity:	0.621	Drug-induced Nephrotoxicity:	0.941
Genotoxicity:	0.695	RPMI-8226 Immunitoxicity:	0.106
A549 Cytotoxicity:	0.794	Hek293 Cytotoxicity:	0.286
BCF:	1.122 ? 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:	3.554 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.178 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.323 ? 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
NPO30412	Kalopanax pictus	Species	Araliaceae	Eukaryota	n.a.	stem	n.a.	PMID[21870831]
NPO30412	Kalopanax pictus	Species	Araliaceae	Eukaryota	stem bark	Purchased from an herbal market at Kumsan, Chungnam, Korea	2009-AUG	PMID[21870831]
NPO30412	Kalopanax pictus	Species	Araliaceae	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
IC50	1

Activity Type	# Activity
Others	1

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
NPT2	Others	Unspecified	n.a.	IC50	=	16400.0	nM	PMID[21870831]

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 NPC306746 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	20448
0.1-0.2	24093
0.2-0.3	4218
0.3-0.4	825
0.4-0.5	169
0.5-0.6	79
0.6-0.7	14
0.7-0.8	0
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8442	Intermediate Similarity	NPC199457
0.8077	Intermediate Similarity	NPC237503
0.7595	Intermediate Similarity	NPC167383
0.7241	Intermediate Similarity	NPC29069
0.6628	Remote Similarity	NPC48249
0.6437	Remote Similarity	NPC68419
0.6374	Remote Similarity	NPC214484
0.6333	Remote Similarity	NPC209894
0.6322	Remote Similarity	NPC37739
0.625	Remote Similarity	NPC604133
0.6211	Remote Similarity	NPC150400
0.6105	Remote Similarity	NPC235405
0.6067	Remote Similarity	NPC137917
0.6064	Remote Similarity	NPC48499
0.6061	Remote Similarity	NPC102439
0.6042	Remote Similarity	NPC249848
0.6042	Remote Similarity	NPC107966
0.6022	Remote Similarity	NPC238935
0.5979	Remote Similarity	NPC295371
0.5979	Remote Similarity	NPC473884
0.5979	Remote Similarity	NPC39211
0.5938	Remote Similarity	NPC475516
0.593	Remote Similarity	NPC191763
0.5909	Remote Similarity	NPC46388
0.59	Remote Similarity	NPC40775
0.59	Remote Similarity	NPC473459
0.5859	Remote Similarity	NPC223301
0.5859	Remote Similarity	NPC171544
0.5842	Remote Similarity	NPC235438
0.5816	Remote Similarity	NPC157868
0.58	Remote Similarity	NPC104071
0.58	Remote Similarity	NPC30735
0.5758	Remote Similarity	NPC469946
0.5743	Remote Similarity	NPC10607
0.57	Remote Similarity	NPC192791
0.57	Remote Similarity	NPC242840
0.57	Remote Similarity	NPC112352
0.5684	Remote Similarity	NPC90856
0.5667	Remote Similarity	NPC116794
0.5652	Remote Similarity	NPC271138
0.5652	Remote Similarity	NPC110139
0.5652	Remote Similarity	NPC108709
0.5631	Remote Similarity	NPC222580
0.5631	Remote Similarity	NPC297263
0.5612	Remote Similarity	NPC139894
0.56	Remote Similarity	NPC473343
0.5588	Remote Similarity	NPC251768
0.5588	Remote Similarity	NPC159309
0.5588	Remote Similarity	NPC46665
0.5588	Remote Similarity	NPC86222
0.5566	Remote Similarity	NPC481030
0.5556	Remote Similarity	NPC473373
0.5534	Remote Similarity	NPC475591
0.5534	Remote Similarity	NPC63159
0.5534	Remote Similarity	NPC236870
0.5524	Remote Similarity	NPC281148
0.5524	Remote Similarity	NPC104372
0.5484	Remote Similarity	NPC102914
0.5481	Remote Similarity	NPC609763
0.5426	Remote Similarity	NPC220984
0.5421	Remote Similarity	NPC80986
0.5408	Remote Similarity	NPC475208
0.5385	Remote Similarity	NPC605954
0.5377	Remote Similarity	NPC114484
0.5376	Remote Similarity	NPC310014
0.5376	Remote Similarity	NPC269315
0.5376	Remote Similarity	NPC64106
0.537	Remote Similarity	NPC31838
0.534	Remote Similarity	NPC109588
0.5327	Remote Similarity	NPC301449
0.5327	Remote Similarity	NPC601290
0.5309	Remote Similarity	NPC246708
0.5268	Remote Similarity	NPC481031
0.5229	Remote Similarity	NPC481078
0.5229	Remote Similarity	NPC187290
0.5213	Remote Similarity	NPC7870
0.5213	Remote Similarity	NPC75747
0.5192	Remote Similarity	NPC309714
0.5182	Remote Similarity	NPC75287
0.5175	Remote Similarity	NPC100639
0.5175	Remote Similarity	NPC470218
0.5161	Remote Similarity	NPC190837
0.5152	Remote Similarity	NPC1046
0.5143	Remote Similarity	NPC305267
0.5138	Remote Similarity	NPC96641
0.5138	Remote Similarity	NPC163183
0.5138	Remote Similarity	NPC241909
0.51	Remote Similarity	NPC179434
0.5088	Remote Similarity	NPC135904
0.5052	Remote Similarity	NPC256798
0.5051	Remote Similarity	NPC189884
0.5051	Remote Similarity	NPC138334
0.5047	Remote Similarity	NPC475504
0.5046	Remote Similarity	NPC481079
0.5044	Remote Similarity	NPC79643
0.5043	Remote Similarity	NPC475160
0.5043	Remote Similarity	NPC473714

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC306746 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7249
0.1-0.2	1834
0.2-0.3	63
0.3-0.4	3
0.4-0.5	1
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