NPASS Compound

Natural Product: NPC471431

Natural Product ID	NPC471431
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	VAIVWWJDJQFIDB-LLHJTMKYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2442987
PubChem CID	25147193
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 2D 183193 0 0 0 0 0 0 0 0999 V2000 -0.5135 -20.4249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7036 -21.3379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5096 -22.6029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0082 -22.5374 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7007 -21.2068 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8946 -19.9418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3961 -20.0074 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2804 -19.3677 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4761 -17.8805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9067 -18.3314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0125 -17.3180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6878 -15.8535 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2571 -15.4026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1513 -16.4161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7655 -16.9902 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5754 -16.0772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8829 -17.4077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3843 -17.4733 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4217 -16.2083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2708 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59 1 0 68 63 1 0 1 88 1 0 1 89 1 0 1 90 1 0 2 91 1 0 3 92 1 0 4 93 1 0 5 94 1 0 6 95 1 0 9 96 1 0 10 97 1 0 11 98 1 0 13 99 1 0 14100 1 0 16101 1 0 17102 1 0 18103 1 0 19104 1 0 20105 1 0 20106 1 0 22107 1 0 23108 1 0 24109 1 0 26110 1 0 27111 1 0 27112 1 0 29113 1 0 30114 1 0 31115 1 0 32116 1 0 34117 1 0 35118 1 0 36119 1 0 37120 1 0 38121 1 0 40122 1 0 40123 1 0 44124 1 0 44125 1 0 44126 1 0 45127 1 0 46128 1 0 47129 1 0 49130 1 0 50131 1 0 50132 1 0 51133 1 0 51134 1 0 53135 1 0 55136 1 0 55137 1 0 55138 1 0 56139 1 0 56140 1 0 56141 1 0 57142 1 0 57143 1 0 58144 1 0 58145 1 0 60146 1 0 61147 1 0 61148 1 0 62149 1 0 62150 1 0 65151 1 0 65152 1 0 66153 1 0 68154 1 0 69155 1 0 69156 1 0 71157 1 0 71158 1 0 72159 1 0 72160 1 0 73161 1 0 73162 1 0 73163 1 0 74164 1 0 76165 1 0 76166 1 0 78167 1 0 79168 1 0 79169 1 0 79170 1 0 80171 1 0 80172 1 0 80173 1 0 81174 1 0 81175 1 0 81176 1 0 82177 1 0 82178 1 0 83179 1 0 84180 1 0 85181 1 0 86182 1 0 87183 1 0 M END

Standard InCHIKey	VAIVWWJDJQFIDB-LLHJTMKYSA-N
Standard InCHI	InChI=1S/C60H96O27/c1-25-36(66)41(71)44(74)50(80-25)85-46-39(69)28(19-61)81-53(48(46)87-49-43(73)37(67)27(64)20-77-49)83-30-22-78-52(47(40(30)70)86-51-45(75)42(72)38(68)29(82-51)21-76-26(2)63)84-35-11-12-56(6)31(54(35,3)4)9-13-57(7)32(56)10-14-60-33-17-55(5,23-62)15-16-59(33,24-79-60)34(65)18-58(57,60)8/h23,25,27-53,61,64-75H,9-22,24H2,1-8H3/t25-,27+,28+,29+,30-,31-,32+,33+,34+,35-,36-,37-,38+,39+,40-,41+,42-,43+,44+,45+,46-,47+,48+,49-,50-,51-,52-,53-,55-,56-,57+,58-,59+,60-/m0/s1
SMILES	CC1C(C(C(C(O1)OC2C(C(OC(C2OC3C(C(C(CO3)O)O)O)OC4COC(C(C4O)OC5C(C(C(C(O5)COC(=O)C)O)O)O)OC6CCC7(C(C6(C)C)CCC8(C7CCC91C8(CC(C2(C9CC(CC2)(C)C=O)CO1)O)C)C)C)CO)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1248.61	Volume:	1184.258 ? Van der Waals volume.
Dense:	1.054	LogP:	-0.386 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.528 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.488 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	15.0	Rigid Bonds:	61.0
TPSA:	407.89 ? Topological Polar Surface Area.	H-Bond Acceptor:	27.0
H-Bond Donor:	13.0	Rings:	11.0
Heavy Atoms:	27.0

MedChem Properties

QED Drug-Likeness Score:	0.049	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.481	Fsp³:	0.967
MCE-18:	316.525 ? 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:	0.021	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.002 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.281 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.395	Promiscuous compounds:	0.005

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.653	MDCK Permeability:	-4.724
Pgp-inhibitor:	0.0	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):	1.0
20% Bioavailability (F20%):	0.735	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	1.0
Plasma Protein Binding (PPB):	27.724%	Volume Distribution (VD):	-0.59
Fu:	39.423% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.0
OATP1B3 inhibitor:	0.147	BCRP inhibitor:	0.0
BSEP inhibitor:	0.04

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.999	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.225	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.022	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
HLM stability:	0.0 ? 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):

-0.694

Half-life (T1/2):

4.138

ADMET: Toxicity

hERG Blockers:	0.014	hERG Blockers (10um):	0.316
Human Hepatotoxicity (H-HT):	0.215	Drug-induced Liver Injury (DILI):	0.159
AMES Toxicity:	0.788	Rat Oral Acute Toxicity:	0.067
Maximum Recommended Daily Dose:	0.126	Skin Sensitization:	0.01
Carcinogencity:	0.011	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.32	Ototoxicity:	1.0
Hematotoxicity:	0.002	Drug-induced Nephrotoxicity:	0.006
Genotoxicity:	0.007	RPMI-8226 Immunitoxicity:	0.157
A549 Cytotoxicity:	0.006	Hek293 Cytotoxicity:	0.89
BCF:	0.23 ? 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:	4.095 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.424 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.306 ? 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
NPO32586	ardisia gigantifolia stapf.	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24095094]
NPO32586	ardisia gigantifolia stapf.	Species	Primulaceae	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	3

Activity Type	# Activity
Cell line	3

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
NPT180	Cell line	HCT-8	Homo sapiens	IC50	=	4100.0	nM	PMID[22472691]
NPT181	Cell line	Bel-7402	Homo sapiens	IC50	=	7760.0	nM	PMID[24025124]
NPT81	Cell line	A549	Homo sapiens	IC50	=	7520.0	nM	PMID[7069725]

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 NPC471431 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	28008
0.1-0.2	19050
0.2-0.3	1951
0.3-0.4	661
0.4-0.5	143
0.5-0.6	5
0.6-0.7	14
0.7-0.8	0
0.8-0.85	3
0.85-0.9	3
0.9-0.95	2
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9286	High Similarity	NPC471426
0.9279	High Similarity	NPC231566
0.8919	High Similarity	NPC262567
0.8621	High Similarity	NPC471427
0.8509	High Similarity	NPC471425
0.8362	Intermediate Similarity	NPC471429
0.8167	Intermediate Similarity	NPC471626
0.8017	Intermediate Similarity	NPC205129
0.7895	Intermediate Similarity	NPC138219
0.7895	Intermediate Similarity	NPC475234
0.7826	Intermediate Similarity	NPC473688
0.7815	Intermediate Similarity	NPC189575
0.7759	Intermediate Similarity	NPC209798
0.7719	Intermediate Similarity	NPC40716
0.7623	Intermediate Similarity	NPC106701
0.76	Intermediate Similarity	NPC471428
0.7561	Intermediate Similarity	NPC471424
0.7477	Intermediate Similarity	NPC158051
0.7288	Intermediate Similarity	NPC475630
0.7179	Intermediate Similarity	NPC77717
0.7094	Intermediate Similarity	NPC158367
0.7094	Intermediate Similarity	NPC253611
0.7094	Intermediate Similarity	NPC488782
0.7016	Intermediate Similarity	NPC66513
0.7009	Intermediate Similarity	NPC119628
0.7008	Intermediate Similarity	NPC471430
0.6891	Remote Similarity	NPC267238
0.6842	Remote Similarity	NPC18724
0.6667	Remote Similarity	NPC471375
0.6638	Remote Similarity	NPC224003
0.6613	Remote Similarity	NPC51579
0.6557	Remote Similarity	NPC148593
0.6557	Remote Similarity	NPC157571
0.6557	Remote Similarity	NPC471373
0.6538	Remote Similarity	NPC22709
0.6417	Remote Similarity	NPC171741
0.6333	Remote Similarity	NPC323231
0.625	Remote Similarity	NPC126753
0.621	Remote Similarity	NPC470623
0.6142	Remote Similarity	NPC471374
0.5952	Remote Similarity	NPC207693
0.5938	Remote Similarity	NPC273189
0.5859	Remote Similarity	NPC184805
0.5781	Remote Similarity	NPC87393
0.5441	Remote Similarity	NPC470622

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC471431 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7878
0.1-0.2	1241
0.2-0.3	30
0.3-0.4	1
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