NPASS Compound

Natural Product: NPC478390

Natural Product ID	NPC478390
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	CIPMGVIJZMPLCL-QHYHZEAJSA-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]

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 51 53 0 0 0 0 0 0 0 0999 V2000 1.3864 0.9395 -2.3579 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7271 0.1230 -1.5532 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0493 -0.9872 -2.1766 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1936 -1.3313 -1.2472 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5777 -0.0426 -0.5416 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0097 -0.0781 -0.1348 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8204 0.1709 -1.4188 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4590 -1.4059 0.4013 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3477 1.0645 0.7922 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2575 2.1126 0.6872 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9390 1.5949 1.1591 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6036 0.2354 0.5526 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6520 -0.7643 1.6770 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7712 0.3223 -0.0729 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7176 -0.7162 0.4825 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0731 -0.5454 -0.1015 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1360 -0.2968 0.6497 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1510 -0.1523 2.1462 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5582 0.2534 2.4068 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0314 0.5933 3.5149 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3059 0.2094 1.2431 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5026 -0.1141 0.1709 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8655 -0.2378 -1.0350 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3379 0.7732 -3.4219 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9622 1.7597 -1.9298 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5788 -1.8613 -2.4125 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5326 -0.5978 -3.1188 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8218 -2.1011 -0.5521 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0410 -1.7708 -1.8037 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4686 0.7671 -1.2966 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7428 0.7186 -1.2056 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9927 -0.8044 -1.9187 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2104 0.8178 -2.1081 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2595 -1.8748 -0.2090 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6247 -2.1661 0.4069 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9088 -1.3129 1.4335 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5082 0.7625 1.8314 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2965 1.5918 0.4799 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5563 2.9430 1.3695 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2260 2.5394 -0.3265 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1572 2.3440 0.8860 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 1.5641 2.2649 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0031 -0.3412 2.4950 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3245 -1.7657 1.4045 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6716 -0.7578 2.0996 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2287 1.3134 0.1235 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8183 -0.5917 1.6005 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4026 -1.7429 0.3096 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2249 -0.6217 -1.1729 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9930 -1.1304 2.6308 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4284 0.5988 2.4942 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 6 8 1 0 6 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 1 12 14 1 0 14 15 1 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 1 0 22 23 2 0 14 2 1 0 22 17 1 0 12 5 1 0 1 24 1 0 1 25 1 0 3 26 1 0 3 27 1 0 4 28 1 0 4 29 1 0 5 30 1 6 7 31 1 0 7 32 1 0 7 33 1 0 8 34 1 0 8 35 1 0 8 36 1 0 9 37 1 0 9 38 1 0 10 39 1 0 10 40 1 0 11 41 1 0 11 42 1 0 13 43 1 0 13 44 1 0 13 45 1 0 14 46 1 6 15 47 1 0 15 48 1 0 16 49 1 0 18 50 1 0 18 51 1 0 M END

Standard InCHIKey	CIPMGVIJZMPLCL-QHYHZEAJSA-N
Standard InCHI	InChI=1S/C20H28O3/c1-13-6-9-16-19(2,3)10-5-11-20(16,4)15(13)8-7-14-12-17(21)23-18(14)22/h7,15-16H,1,5-6,8-12H2,2-4H3/b14-7+/t15-,16-,20+/m0/s1
SMILES	C=C1CC[C@H]2C(C)(C)CCC[C@]2(C)[C@H]1C/C=C/1CC(=O)OC1=O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	316.2	Volume:	344.632 ? Van der Waals volume.
Dense:	0.918	LogP:	4.159 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.723 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.925 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	2.0	Rigid Bonds:	20.0
TPSA:	43.37 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	0.0	Rings:	3.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.324	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.365	Fsp³:	0.7
MCE-18:	54.353 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.332	Fluc inhibitor:	0.284 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.004 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.003 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.911	Promiscuous compounds:	0.063

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.435	MDCK Permeability:	-4.794
Pgp-inhibitor:	0.804	Pgp-substrate:	0.0
PAMPA:	0.011 ? 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):	0.0
20% Bioavailability (F20%):	0.001	30% Bioavailability (F30%):	0.008
50% Bioavailability (F50%):	0.2

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003	MRP1:	0.02
Plasma Protein Binding (PPB):	98.16%	Volume Distribution (VD):	0.058
Fu:	1.71% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.015
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.464	CYP1A2-substrate:	0.069
CYP2C19-inhibitor:	0.985	CYP2C19-substrate:	0.02
CYP2C9-inhibitor:	0.081	CYP2C9-substrate:	0.008
CYP2D6-inhibitor:	0.473	CYP2D6-substrate:	0.501
CYP3A4-inhibitor:	0.661	CYP3A4-substrate:	0.026
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.995
HLM stability:	0.999 ? 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):

4.501

Half-life (T1/2):

0.786

ADMET: Toxicity

hERG Blockers:	0.06	hERG Blockers (10um):	0.219
Human Hepatotoxicity (H-HT):	0.675	Drug-induced Liver Injury (DILI):	0.819
AMES Toxicity:	0.138	Rat Oral Acute Toxicity:	0.292
Maximum Recommended Daily Dose:	0.77	Skin Sensitization:	0.988
Carcinogencity:	0.49	Eye Corrosion:	0.1
Eye Irritation:	0.818	Respiratory Toxicity:	0.358
Drug-induced Neurotoxicity:	0.568	Ototoxicity:	0.585
Hematotoxicity:	0.48	Drug-induced Nephrotoxicity:	0.966
Genotoxicity:	0.872	RPMI-8226 Immunitoxicity:	0.051
A549 Cytotoxicity:	0.042	Hek293 Cytotoxicity:	0.137
BCF:	1.962 ? 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:	4.772 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.528 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	6.22 ? 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
NPO41076	Amomum villosum	Species	Zingiberaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[31710213]
NPO41076	Amomum villosum	Species	Zingiberaceae	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	2
Inhibition	1

Activity Type	# Activity
Cell line	1
Others	2

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
NPT113	Cell line	RAW264.7	Mus musculus	IC50	=	11000.0	nM	PMID[31710213]
NPT2	Others	Unspecified	n.a.	Inhibition	=	90.3	%	PMID[31710213]
NPT2	Others	Unspecified	n.a.	IC50	=	21100.0	nM	PMID[31710213]

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 NPC478390 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	22327
0.1-0.2	23589
0.2-0.3	3470
0.3-0.4	376
0.4-0.5	62
0.5-0.6	18
0.6-0.7	9
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	Natural Product ID
0.7551	Intermediate Similarity	NPC12170
0.74	Intermediate Similarity	NPC217394
0.7115	Intermediate Similarity	NPC469
0.7115	Intermediate Similarity	NPC478393
0.6863	Remote Similarity	NPC144947
0.6852	Remote Similarity	NPC478394
0.6604	Remote Similarity	NPC79027
0.64	Remote Similarity	NPC169275
0.64	Remote Similarity	NPC52449
0.6275	Remote Similarity	NPC175334
0.6226	Remote Similarity	NPC251528
0.6111	Remote Similarity	NPC238146
0.6038	Remote Similarity	NPC99321
0.5769	Remote Similarity	NPC185587
0.5714	Remote Similarity	NPC75485
0.5714	Remote Similarity	NPC168975
0.566	Remote Similarity	NPC189745
0.566	Remote Similarity	NPC35655
0.5614	Remote Similarity	NPC475709
0.5385	Remote Similarity	NPC268039
0.537	Remote Similarity	NPC484731
0.5345	Remote Similarity	NPC311070
0.5345	Remote Similarity	NPC472809
0.5345	Remote Similarity	NPC177037
0.5345	Remote Similarity	NPC472810
0.5345	Remote Similarity	NPC472814
0.5333	Remote Similarity	NPC478391
0.5227	Remote Similarity	NPC103290
0.52	Remote Similarity	NPC60772
0.5085	Remote Similarity	NPC478375
0.5082	Remote Similarity	NPC489288

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC478390 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7335
0.1-0.2	1728
0.2-0.3	83
0.3-0.4	1
0.4-0.5	3
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