NPASS Compound

Natural Product: NPC92149

Natural Product ID	NPC92149
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	PBVMPAHKYVXSHF-UHFFFAOYSA-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] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0002586] O-methylated isoflavonoids [CHEMONTID:0002606] 4'-O-methylated isoflavonoids [CHEMONTID:0003651] 3'-hydroxy,4'-methoxyisoflavonoids

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 42 44 0 0 0 0 0 0 0 0999 V2000 -1.5243 -3.4085 -0.7339 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8377 -2.2094 -0.5827 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5292 -1.0111 -0.3893 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9085 -1.0238 -0.3488 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6051 0.1674 -0.1563 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9085 1.3247 -0.0115 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5266 1.3978 -0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8688 0.1948 -0.2364 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5815 0.1664 -0.2854 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2143 0.3253 -1.4985 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5106 0.3047 -1.5723 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2307 0.1331 -0.4977 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6179 0.1132 -0.5903 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4461 -0.0626 0.4961 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8762 -0.2272 1.7377 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5039 -0.2107 1.8516 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6832 -0.0342 0.7591 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3058 -0.0168 0.8682 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7562 -0.1676 2.0099 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9596 -0.3791 3.1165 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8360 -0.0800 0.3850 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8257 2.5613 0.1021 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4053 3.4605 -0.8379 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5943 2.5079 0.1795 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9738 0.0881 -0.1256 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6919 -1.1190 -0.2765 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2455 -3.3049 -1.5965 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8229 -4.2099 -1.0455 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0252 -3.7769 0.1794 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4499 -1.9519 -0.4654 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6321 0.4729 -2.4284 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0329 0.2457 -1.5816 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5205 -0.3678 2.6093 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3074 0.2258 3.8511 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3324 0.6749 0.8633 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4407 2.9888 -1.8470 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6840 3.6893 -0.6512 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9158 4.4262 -0.8791 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3621 2.4626 0.8683 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4554 -1.8696 0.4855 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3377 -1.5559 -1.2554 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7764 -0.9450 -0.4257 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 16 20 1 0 14 21 1 0 7 22 1 0 22 23 1 0 6 24 1 0 5 25 1 0 25 26 1 0 8 3 1 0 18 9 1 0 17 12 1 0 1 27 1 0 1 28 1 0 1 29 1 0 4 30 1 0 10 31 1 0 13 32 1 0 15 33 1 0 20 34 1 0 21 35 1 0 23 36 1 0 23 37 1 0 23 38 1 0 24 39 1 0 26 40 1 0 26 41 1 0 26 42 1 0 M END

Standard InCHIKey	PBVMPAHKYVXSHF-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C18H16O8/c1-23-11-6-13(24-2)17(22)18(25-3)14(11)9-7-26-12-5-8(19)4-10(20)15(12)16(9)21/h4-7,19-20,22H,1-3H3
SMILES	COc1cc(c(c(c1c1coc2cc(cc(c2c1=O)O)O)OC)O)OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	360.08	Volume:	343.445 ? Van der Waals volume.
Dense:	1.048	LogP:	1.54 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.777 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.818 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	18.0
TPSA:	118.59 ? Topological Polar Surface Area.	H-Bond Acceptor:	8.0
H-Bond Donor:	3.0	Rings:	3.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.65	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.703	Fsp³:	0.167
MCE-18:	20.0 ? 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:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	1	PAINS Alert:	0
Colloidal aggregators:	0.295	Fluc inhibitor:	0.161 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.523 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.43 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.354	Promiscuous compounds:	0.861

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.276	MDCK Permeability:	-4.833
Pgp-inhibitor:	0.257	Pgp-substrate:	0.269
PAMPA:	0.017 ? 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):	0.018
20% Bioavailability (F20%):	0.112	30% Bioavailability (F30%):	0.43
50% Bioavailability (F50%):	0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.022	MRP1:	0.917
Plasma Protein Binding (PPB):	96.015%	Volume Distribution (VD):	-0.432
Fu:	3.656% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.987
OATP1B3 inhibitor:	0.995	BCRP inhibitor:	0.995
BSEP inhibitor:	0.55

ADMET: Metabolism

CYP1A2-inhibitor:	0.999	CYP1A2-substrate:	0.719
CYP2C19-inhibitor:	0.783	CYP2C19-substrate:	0.278
CYP2C9-inhibitor:	0.992	CYP2C9-substrate:	0.338
CYP2D6-inhibitor:	0.997	CYP2D6-substrate:	0.998
CYP3A4-inhibitor:	0.007	CYP3A4-substrate:	0.191
CYP2B6-substrate:	0.003	CYP2C8-inhibitor:	0.926
HLM stability:	0.955 ? 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):

3.71

Half-life (T1/2):

1.663

ADMET: Toxicity

hERG Blockers:	0.093	hERG Blockers (10um):	0.5
Human Hepatotoxicity (H-HT):	0.481	Drug-induced Liver Injury (DILI):	0.814
AMES Toxicity:	0.51	Rat Oral Acute Toxicity:	0.56
Maximum Recommended Daily Dose:	0.805	Skin Sensitization:	0.418
Carcinogencity:	0.752	Eye Corrosion:	0.029
Eye Irritation:	0.975	Respiratory Toxicity:	0.804
Drug-induced Neurotoxicity:	0.15	Ototoxicity:	0.18
Hematotoxicity:	0.166	Drug-induced Nephrotoxicity:	0.12
Genotoxicity:	0.892	RPMI-8226 Immunitoxicity:	0.118
A549 Cytotoxicity:	0.281	Hek293 Cytotoxicity:	0.589
BCF:	1.002 ? 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:	3.588 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.486 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.827 ? 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
NPO15828	Garcinia nervosa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15828	Garcinia nervosa	Species	Clusiaceae	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

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

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 NPC92149 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	29995
0.1-0.2	17015
0.2-0.3	2240
0.3-0.4	473
0.4-0.5	103
0.5-0.6	15
0.6-0.7	16
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
0.7119	Intermediate Similarity	NPC142876
0.6842	Remote Similarity	NPC78341
0.661	Remote Similarity	NPC19980
0.661	Remote Similarity	NPC239363
0.6441	Remote Similarity	NPC294409
0.6441	Remote Similarity	NPC490701
0.6393	Remote Similarity	NPC278323
0.6393	Remote Similarity	NPC194653
0.629	Remote Similarity	NPC254702
0.629	Remote Similarity	NPC45291
0.623	Remote Similarity	NPC309154
0.623	Remote Similarity	NPC200316
0.6129	Remote Similarity	NPC279668
0.6129	Remote Similarity	NPC481044
0.6094	Remote Similarity	NPC167595
0.6032	Remote Similarity	NPC483637
0.6032	Remote Similarity	NPC264550
0.5789	Remote Similarity	NPC193792
0.569	Remote Similarity	NPC39426
0.569	Remote Similarity	NPC608554
0.5652	Remote Similarity	NPC280937
0.5652	Remote Similarity	NPC128774
0.5507	Remote Similarity	NPC233918
0.5507	Remote Similarity	NPC268059
0.55	Remote Similarity	NPC87545
0.55	Remote Similarity	NPC38065
0.5493	Remote Similarity	NPC482075
0.5455	Remote Similarity	NPC104728
0.5429	Remote Similarity	NPC479305
0.5325	Remote Similarity	NPC481043
0.5075	Remote Similarity	NPC476055
0.5068	Remote Similarity	NPC74178

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC92149 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5851
0.1-0.2	3263
0.2-0.3	32
0.3-0.4	3
0.4-0.5	0
0.5-0.6	1
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
0.569	Remote Similarity	NPD1510	Phase 2

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