NPASS Compound

Natural Product: NPC116513

Natural Product ID	NPC116513
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Bipinnatone A
IUPAC Name	3-[4-hydroxy-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl]phenyl]-1-(2,4,6-trihydroxyphenyl)propan-1-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL525006
PubChem CID	25016410
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003467] Linear 1,3-diarylpropanoids [CHEMONTID:0001630] Chalcones and dihydrochalcones [CHEMONTID:0003473] 2'-Hydroxy-dihydrochalcones

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 73 74 0 0 0 0 0 0 0 0999 V2000 0.6591 1.7337 1.1394 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2847 0.5486 1.7574 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5872 -0.3995 2.3120 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8452 -0.5798 2.4821 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7921 0.4052 2.0200 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5639 0.2053 0.8691 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4793 1.1367 0.4761 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2737 0.8741 -0.7590 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5211 0.1488 -0.3728 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3781 -0.1544 -1.5586 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9562 0.2152 -2.6830 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6463 -0.8429 -1.4506 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8067 -0.1312 -1.2658 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7615 1.2528 -1.1815 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.0419 -0.7408 -1.1574 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.0631 -2.1281 -1.2446 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.9219 -2.8874 -1.4303 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7154 -2.2129 -1.5311 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5390 -2.9166 -1.7173 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.2865 -2.7797 -1.1404 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6654 2.3018 1.2084 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9126 2.5055 2.3388 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9863 1.5756 2.7467 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2388 1.8006 3.8894 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7957 0.4507 1.7629 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2696 0.3974 0.3403 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7565 0.2945 0.2987 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4741 1.2013 -0.2915 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9295 1.2729 -0.4381 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7533 0.1721 0.0840 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5987 -1.1512 -0.5374 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6080 -1.7980 -1.1160 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3872 -3.1197 -1.7199 C 0 0 0 0 0 0 0 0 0 0 0 0 9.9410 -1.1648 -1.1378 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7071 2.3534 -0.9202 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4856 2.5525 1.9023 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1936 1.5255 0.5138 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4172 2.2033 0.4247 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2239 -1.2412 2.7411 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0108 -0.8132 3.6035 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0940 -1.6225 2.0524 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4088 -0.6978 0.3162 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6760 0.2370 -1.4236 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4859 1.8189 -1.2993 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2011 -0.8374 0.0754 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1088 0.6621 0.4029 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3646 1.7790 -1.8011 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.9656 -0.2013 -1.0124 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.9442 -3.9668 -1.4975 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8688 -2.5620 -2.3690 H 0 0 0 0 0 0 0 0 0 0 0 0 -12.0916 -2.3629 -0.6749 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3952 3.0228 0.8773 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0525 3.4197 2.9220 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6390 1.0980 4.2925 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1040 -0.4656 2.2701 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2075 1.3661 2.2565 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8834 -0.5876 -0.0679 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8756 1.1540 -0.3255 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1957 -0.5426 0.7921 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2425 2.2032 0.1403 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1797 1.5602 -1.4932 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5427 0.0914 1.1903 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8285 0.4759 0.0083 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6343 -1.6330 -0.5398 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2729 -3.8924 -0.9094 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1866 -3.4512 -2.3861 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4090 -3.0974 -2.2513 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9268 -0.2023 -1.6963 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3174 -0.9253 -0.1095 H 0 0 0 0 0 0 0 0 0 0 0 0 10.7035 -1.7961 -1.6448 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1094 1.9131 -1.7476 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3715 3.1596 -1.2573 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0259 2.8170 -0.1725 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 10 12 1 0 12 13 2 0 13 14 1 0 13 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 16 20 1 0 7 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 2 25 1 0 25 26 1 0 26 27 1 0 27 28 2 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 2 3 32 33 1 0 32 34 1 0 28 35 1 0 23 5 1 0 18 12 1 0 1 36 1 0 1 37 1 0 1 38 1 0 3 39 1 0 4 40 1 0 4 41 1 0 6 42 1 0 8 43 1 0 8 44 1 0 9 45 1 0 9 46 1 0 14 47 1 0 15 48 1 0 17 49 1 0 19 50 1 0 20 51 1 0 21 52 1 0 22 53 1 0 24 54 1 0 25 55 1 0 25 56 1 0 26 57 1 0 26 58 1 0 27 59 1 0 29 60 1 0 29 61 1 0 30 62 1 0 30 63 1 0 31 64 1 0 33 65 1 0 33 66 1 0 33 67 1 0 34 68 1 0 34 69 1 0 34 70 1 0 35 71 1 0 35 72 1 0 35 73 1 0 M END

Standard InCHIKey	SJBBGMVJNAOUOI-VLURGLOZSA-N
Standard InCHI	InChI=1S/C30H38O5/c1-20(2)7-5-8-21(3)9-6-10-22(4)11-14-24-17-23(12-15-26(24)32)13-16-27(33)30-28(34)18-25(31)19-29(30)35/h7,9,11-12,15,17-19,31-32,34-35H,5-6,8,10,13-14,16H2,1-4H3/b21-9+,22-11+
SMILES	C/C(=CCc1cc(CCC(=O)c2c(O)cc(cc2O)O)ccc1O)/CC/C=C(/CCC=C(C)C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	478.27	Volume:	527.91 ? Van der Waals volume.
Dense:	0.906	LogP:	8.325 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.3 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.182 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	12.0	Rigid Bonds:	16.0
TPSA:	97.99 ? Topological Polar Surface Area.	H-Bond Acceptor:	5.0
H-Bond Donor:	4.0	Rings:	2.0
Heavy Atoms:	5.0

MedChem Properties

QED Drug-Likeness Score:	0.19	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.051	Fsp³:	0.367
MCE-18:	17.0 ? 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:	0.997	Fluc inhibitor:	0.279 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.3 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.334 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.638	Promiscuous compounds:	0.077

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.883	MDCK Permeability:	-4.772
Pgp-inhibitor:	1.0	Pgp-substrate:	0.0
PAMPA:	0.002 ? 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%):	0.009	30% Bioavailability (F30%):	0.731
50% Bioavailability (F50%):	0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.958
Plasma Protein Binding (PPB):	97.061%	Volume Distribution (VD):	0.243
Fu:	2.706% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.049
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.029	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.958	CYP2C19-substrate:	1.0
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.998
CYP2D6-inhibitor:	1.0	CYP2D6-substrate:	0.999
CYP3A4-inhibitor:	0.005	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	1.0 ? 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):

7.509

Half-life (T1/2):

0.992

ADMET: Toxicity

hERG Blockers:	0.132	hERG Blockers (10um):	0.736
Human Hepatotoxicity (H-HT):	0.714	Drug-induced Liver Injury (DILI):	0.049
AMES Toxicity:	0.055	Rat Oral Acute Toxicity:	0.369
Maximum Recommended Daily Dose:	0.693	Skin Sensitization:	0.971
Carcinogencity:	0.062	Eye Corrosion:	0.0
Eye Irritation:	0.859	Respiratory Toxicity:	0.992
Drug-induced Neurotoxicity:	0.321	Ototoxicity:	0.4
Hematotoxicity:	0.155	Drug-induced Nephrotoxicity:	0.281
Genotoxicity:	0.88	RPMI-8226 Immunitoxicity:	0.09
A549 Cytotoxicity:	0.78	Hek293 Cytotoxicity:	0.813
BCF:	2.273 ? 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:	5.801 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	7.313 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	7.064 ? 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
NPO19134	Boronia bipinnata	Species	Rutaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[18662038]
NPO19134	Boronia bipinnata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19134	Boronia bipinnata	Species	Rutaceae	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

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	=	64000.0	nM	PMID[18662038]

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 NPC116513 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	16862
0.1-0.2	29010
0.2-0.3	3466
0.3-0.4	430
0.4-0.5	71
0.5-0.6	15
0.6-0.7	1
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9623	High Similarity	NPC267846
0.6774	Remote Similarity	NPC483966
0.5507	Remote Similarity	NPC483963
0.5439	Remote Similarity	NPC233056
0.5424	Remote Similarity	NPC260775
0.5424	Remote Similarity	NPC130756
0.5424	Remote Similarity	NPC70677
0.5424	Remote Similarity	NPC12931
0.5385	Remote Similarity	NPC601448
0.5357	Remote Similarity	NPC242895
0.5342	Remote Similarity	NPC96408
0.5342	Remote Similarity	NPC610511
0.5333	Remote Similarity	NPC91105
0.5231	Remote Similarity	NPC4493
0.5211	Remote Similarity	NPC290030
0.5156	Remote Similarity	NPC601405
0.5085	Remote Similarity	NPC152097

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC116513 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4035
0.1-0.2	5010
0.2-0.3	100
0.3-0.4	5
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