NPASS Compound

Natural Product: NPC224641

Natural Product ID	NPC224641
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	JFVYPWSFDLYZKB-XTHGXZEWSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	15214881
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001640] Naphthopyrans

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 65 70 0 0 0 0 0 0 0 0999 V2000 6.5759 1.1013 0.1234 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6173 0.2343 0.9077 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1580 -1.1881 0.8570 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2996 0.2371 0.2163 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6901 1.5912 0.1362 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2392 2.6282 0.5875 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3818 1.6417 -0.5157 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7406 0.4716 -0.5987 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4202 0.4346 -1.2392 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0127 1.7367 -1.8066 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4355 1.5777 -2.3704 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2655 1.2074 -1.2199 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7415 1.0939 -1.4001 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0753 0.2731 -0.1881 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0415 -0.0216 0.7313 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3375 0.4100 0.9289 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1034 -0.0717 1.9687 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6048 -0.9994 2.8467 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3136 -1.4541 2.6809 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5568 -0.9647 1.6367 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2959 -1.2364 1.2585 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.9798 -0.5001 0.1560 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9202 -0.2172 -0.8054 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0378 -1.1849 -1.9504 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5418 -0.2178 -0.2783 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5027 0.3708 1.0973 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0387 -1.6649 -0.1511 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2988 -1.7017 0.5446 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3105 -0.7912 -0.0690 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8845 -1.4734 -1.1632 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3506 -0.5774 0.8319 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5352 0.6839 2.2240 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6163 0.7178 0.1698 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2003 1.1738 -0.9160 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5211 2.1470 0.5411 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5285 -1.8383 1.4994 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2288 -1.2208 1.1042 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9867 -1.5404 -0.2003 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4510 -0.1153 -0.8216 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9865 2.5663 -0.8924 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5142 -0.2837 -2.1075 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6813 2.0250 -2.5960 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1163 2.5250 -1.0161 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7466 2.6045 -2.7189 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4641 0.9246 -3.2398 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0650 1.8750 -0.3756 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2145 2.0968 -1.3567 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0761 0.5221 -2.2603 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7083 1.1431 0.2218 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1180 0.2931 2.0897 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2476 -1.3585 3.6628 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9557 -2.1852 3.3929 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6846 -1.9168 1.7629 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2790 -1.0369 -2.7170 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0178 -1.2118 -2.4273 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8652 -2.2014 -1.5188 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3714 0.9871 1.3126 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5123 -0.4418 1.8826 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4117 0.9846 1.3393 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1439 -2.0674 -1.1894 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7543 -2.2866 0.4008 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6814 -2.7487 0.4248 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2025 -1.5191 1.6382 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9416 -0.9013 -1.9481 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4836 0.8592 2.5047 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 2 0 5 7 1 0 7 8 2 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 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 6 23 25 1 0 25 26 1 1 25 27 1 0 27 28 1 0 28 29 1 0 29 30 1 6 29 31 1 0 2 32 1 0 31 4 1 0 29 8 1 0 25 9 1 0 23 12 1 0 22 14 2 0 20 15 1 0 1 33 1 0 1 34 1 0 1 35 1 0 3 36 1 0 3 37 1 0 3 38 1 0 4 39 1 6 7 40 1 0 9 41 1 6 10 42 1 0 10 43 1 0 11 44 1 0 11 45 1 0 12 46 1 1 13 47 1 0 13 48 1 0 16 49 1 0 17 50 1 0 18 51 1 0 19 52 1 0 21 53 1 0 24 54 1 0 24 55 1 0 24 56 1 0 26 57 1 0 26 58 1 0 26 59 1 0 27 60 1 0 27 61 1 0 28 62 1 0 28 63 1 0 30 64 1 0 32 65 1 0 M END

Standard InCHIKey	JFVYPWSFDLYZKB-XTHGXZEWSA-N
Standard InCHI	InChI=1S/C27H33NO4/c1-24(2,30)23-21(29)14-19-18-10-9-15-13-17-16-7-5-6-8-20(16)28-22(17)26(15,4)25(18,3)11-12-27(19,31)32-23/h5-8,14-15,18,23,28,30-31H,9-13H2,1-4H3/t15-,18-,23-,25-,26+,27-/m0/s1
SMILES	CC(C)([C@@H]1C(=O)C=C2[C@@H]3CC[C@H]4Cc5c6ccccc6[nH]c5[C@]4(C)[C@@]3(C)CC[C@]2(O)O1)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	435.24	Volume:	454.548 ? Van der Waals volume.
Dense:	0.958	LogP:	3.077 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.084 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.373 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	1.0	Rigid Bonds:	30.0
TPSA:	82.55 ? Topological Polar Surface Area.	H-Bond Acceptor:	5.0
H-Bond Donor:	3.0	Rings:	6.0
Heavy Atoms:	5.0

MedChem Properties

QED Drug-Likeness Score:	0.628	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.755	Fsp³:	0.593
MCE-18:	136.953 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.247	Fluc inhibitor:	0.022 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.577 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.107 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.009	Promiscuous compounds:	0.841

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.087	MDCK Permeability:	-4.758
Pgp-inhibitor:	0.935	Pgp-substrate:	0.02
PAMPA:	0.073 ? 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%):	0.022	30% Bioavailability (F30%):	0.403
50% Bioavailability (F50%):	0.915

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.022	MRP1:	0.102
Plasma Protein Binding (PPB):	96.309%	Volume Distribution (VD):	0.029
Fu:	3.349% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.442
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.997	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.564	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.004	CYP2C9-substrate:	0.094
CYP2D6-inhibitor:	0.421	CYP2D6-substrate:	0.002
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.998
HLM stability:	0.1 ? 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):

8.577

Half-life (T1/2):

1.287

ADMET: Toxicity

hERG Blockers:	0.203	hERG Blockers (10um):	0.272
Human Hepatotoxicity (H-HT):	0.71	Drug-induced Liver Injury (DILI):	0.324
AMES Toxicity:	0.443	Rat Oral Acute Toxicity:	0.674
Maximum Recommended Daily Dose:	0.926	Skin Sensitization:	0.991
Carcinogencity:	0.798	Eye Corrosion:	0.0
Eye Irritation:	0.17	Respiratory Toxicity:	0.451
Drug-induced Neurotoxicity:	0.097	Ototoxicity:	0.599
Hematotoxicity:	0.214	Drug-induced Nephrotoxicity:	0.911
Genotoxicity:	0.971	RPMI-8226 Immunitoxicity:	0.172
A549 Cytotoxicity:	0.036	Hek293 Cytotoxicity:	0.739
BCF:	1.796 ? 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:	4.248 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.853 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.223 ? 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
NPO40587	Penicillium sp. (strain ZO-R1-1)	Strain	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31117519]
NPO40587	Penicillium sp. (strain ZO-R1-1)	Strain	Aspergillaceae	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	6

Activity Type	# Activity
Cell line	2
Organism	4

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
NPT1864	Cell line	L5178Y	Mus musculus	IC50	=	6200.0	nM	PMID[31117519]
NPT71	Cell line	HEK293	Homo sapiens	IC50	=	39800.0	nM	PMID[31117519]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	153000.0	nM	PMID[37257055]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	1100.0	nM	PMID[37257055]

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 NPC224641 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	10495
0.1-0.2	37776
0.2-0.3	1370
0.3-0.4	163
0.4-0.5	26
0.5-0.6	21
0.6-0.7	5
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
0.7195	Intermediate Similarity	NPC123019
0.6989	Remote Similarity	NPC604787
0.6824	Remote Similarity	NPC484483
0.6163	Remote Similarity	NPC34271
0.6163	Remote Similarity	NPC20697
0.6023	Remote Similarity	NPC235900
0.5824	Remote Similarity	NPC471284
0.5824	Remote Similarity	NPC486860
0.5824	Remote Similarity	NPC602114
0.5814	Remote Similarity	NPC487209
0.5783	Remote Similarity	NPC165201
0.5698	Remote Similarity	NPC487208
0.5667	Remote Similarity	NPC487207
0.549	Remote Similarity	NPC607140
0.5455	Remote Similarity	NPC231342
0.5455	Remote Similarity	NPC609321
0.5426	Remote Similarity	NPC611491
0.5393	Remote Similarity	NPC119700
0.5357	Remote Similarity	NPC99428
0.5326	Remote Similarity	NPC484479
0.5227	Remote Similarity	NPC6093
0.5208	Remote Similarity	NPC601305
0.5114	Remote Similarity	NPC97525
0.5114	Remote Similarity	NPC198339
0.5109	Remote Similarity	NPC487205
0.5106	Remote Similarity	NPC18661
0.5057	Remote Similarity	NPC602195

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC224641 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4204
0.1-0.2	4809
0.2-0.3	136
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