NPASS Compound

Natural Product: NPC122501

Natural Product ID	NPC122501
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	RNJHIYAJJKOFIO-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	10889963
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0000151] Anthraquinones [CHEMONTID:0001598] Hydroxyanthraquinones

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 28 30 0 0 0 0 0 0 0 0999 V2000 4.3193 0.9006 -0.0807 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9671 0.2537 -0.0757 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8358 1.0275 -0.1887 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5528 0.4949 -0.1912 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3941 -0.8514 -0.0774 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5218 -1.6600 0.0386 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7979 -1.1034 0.0387 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9202 -1.9180 0.1549 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9572 -1.4256 -0.0788 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0600 -2.6842 0.0293 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1347 -0.5803 -0.2000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3810 -1.1625 -0.1966 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5361 -0.3745 -0.3118 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3935 1.0051 -0.4292 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1187 1.5340 -0.4267 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9817 0.7791 -0.3152 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6297 1.3588 -0.3142 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5006 2.6018 -0.4199 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4635 1.5112 -0.9958 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0978 0.1341 -0.0098 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3912 1.5571 0.8110 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8840 2.1117 -0.2834 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3896 -2.7251 0.1283 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5065 -1.9706 0.9591 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5490 -2.2127 -0.1096 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5209 -0.8414 -0.3086 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2779 1.6320 -0.5195 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0005 2.6083 -0.5179 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 2 0 5 6 1 0 6 7 2 0 7 8 1 0 5 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 7 2 1 0 16 11 1 0 17 4 1 0 1 19 1 0 1 20 1 0 1 21 1 0 3 22 1 0 6 23 1 0 8 24 1 0 12 25 1 0 13 26 1 0 14 27 1 0 15 28 1 0 M END

Standard InCHIKey	RNJHIYAJJKOFIO-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C15H10O3/c1-8-6-11-12(7-13(8)16)15(18)10-5-3-2-4-9(10)14(11)17/h2-7,16H,1H3
SMILES	Cc1cc2c(cc1O)C(=O)c1ccccc1C2=O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	238.06	Volume:	247.606 ? Van der Waals volume.
Dense:	0.961	LogP:	3.522 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.196 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.91 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	0.0	Rigid Bonds:	18.0
TPSA:	54.37 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	1.0	Rings:	3.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.654	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.98	Fsp³:	0.067
MCE-18:	34.0 ? 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:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	1
Colloidal aggregators:	0.282	Fluc inhibitor:	0.576 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.218 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.316 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.791	Promiscuous compounds:	0.212

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.358	MDCK Permeability:	-4.666
Pgp-inhibitor:	0.935	Pgp-substrate:	0.025
PAMPA:	0.688 ? 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):	0.003
20% Bioavailability (F20%):	0.002	30% Bioavailability (F30%):	0.075
50% Bioavailability (F50%):	0.391

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.012	MRP1:	0.672
Plasma Protein Binding (PPB):	96.328%	Volume Distribution (VD):	0.383
Fu:	3.801% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.943
OATP1B3 inhibitor:	0.552	BCRP inhibitor:	0.006
BSEP inhibitor:	0.461

ADMET: Metabolism

CYP1A2-inhibitor:	1.0	CYP1A2-substrate:	0.026
CYP2C19-inhibitor:	0.322	CYP2C19-substrate:	0.091
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.586
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.752
CYP3A4-inhibitor:	0.02	CYP3A4-substrate:	0.007
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.989
HLM stability:	0.416 ? 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):

8.626

Half-life (T1/2):

0.943

ADMET: Toxicity

hERG Blockers:	0.156	hERG Blockers (10um):	0.657
Human Hepatotoxicity (H-HT):	0.68	Drug-induced Liver Injury (DILI):	0.727
AMES Toxicity:	0.811	Rat Oral Acute Toxicity:	0.358
Maximum Recommended Daily Dose:	0.451	Skin Sensitization:	0.835
Carcinogencity:	0.849	Eye Corrosion:	0.037
Eye Irritation:	0.995	Respiratory Toxicity:	0.663
Drug-induced Neurotoxicity:	0.598	Ototoxicity:	0.233
Hematotoxicity:	0.582	Drug-induced Nephrotoxicity:	0.285
Genotoxicity:	0.508	RPMI-8226 Immunitoxicity:	0.09
A549 Cytotoxicity:	0.458	Hek293 Cytotoxicity:	0.463
BCF:	1.631 ? 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:	4.462 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.546 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.021 ? 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
NPO487	Tabebuia avellanedae	Species	Bignoniaceae	Eukaryota	n.a.	bark	n.a.	PMID[17950604]
NPO487	Tabebuia avellanedae	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17950604]
NPO487	Tabebuia avellanedae	Species	Bignoniaceae	Eukaryota	n.a.	Brazilian	n.a.	PMID[19674905]
NPO487	Tabebuia avellanedae	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32044231]
NPO30972	Morinda officinalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO487	Tabebuia avellanedae	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3751	Orthantha lutea	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15479	Oldenlandia diffusa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO30972	Morinda officinalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15479	Oldenlandia diffusa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15479	Oldenlandia diffusa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15479	Oldenlandia diffusa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30972	Morinda officinalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15479	Oldenlandia diffusa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15479	Oldenlandia diffusa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3751	Orthantha lutea	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO487	Tabebuia avellanedae	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12083	Hydnellum zonatum	Species	Thelephoraceae	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 NPC122501 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	23985
0.1-0.2	21667
0.2-0.3	3890
0.3-0.4	254
0.4-0.5	39
0.5-0.6	16
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
0.6667	Remote Similarity	NPC93015
0.6389	Remote Similarity	NPC258502
0.625	Remote Similarity	NPC602077
0.6111	Remote Similarity	NPC53206
0.6111	Remote Similarity	NPC73061
0.5946	Remote Similarity	NPC608942
0.5833	Remote Similarity	NPC142956
0.5714	Remote Similarity	NPC126767
0.5714	Remote Similarity	NPC120545
0.5556	Remote Similarity	NPC604031
0.5455	Remote Similarity	NPC289883
0.5366	Remote Similarity	NPC67172
0.5349	Remote Similarity	NPC84571
0.5294	Remote Similarity	NPC96915
0.5278	Remote Similarity	NPC300274
0.5263	Remote Similarity	NPC44437
0.525	Remote Similarity	NPC136588
0.5172	Remote Similarity	NPC19256
0.5143	Remote Similarity	NPC599895
0.5128	Remote Similarity	NPC203063
0.5128	Remote Similarity	NPC201542

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC122501 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3619
0.1-0.2	5123
0.2-0.3	391
0.3-0.4	16
0.4-0.5	1
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