NPASS Compound

Natural Product: NPC43644

Natural Product ID	NPC43644
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	WXULKGXQMWVWMP-QGZVFWFLSA-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:0000145] Coumarins and derivatives [CHEMONTID:0000358] Furanocoumarins [CHEMONTID:0002569] Linear furanocoumarins [CHEMONTID:0000202] Psoralens

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 50 52 0 0 0 0 0 0 0 0999 V2000 4.8941 2.9746 -0.8712 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0319 1.8003 -1.1668 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2541 1.2381 -0.2655 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2591 1.8235 1.0951 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4460 0.0940 -0.6448 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4774 -0.3603 -1.8017 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5931 -0.5753 0.2189 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8076 -1.6751 -0.1205 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6391 -1.2456 0.0452 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9598 -0.1531 -0.7906 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2536 0.3318 -0.7306 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5761 1.3288 0.1624 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5975 1.8315 0.9882 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9594 2.8296 1.8693 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2698 3.2631 1.8725 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6077 4.1876 2.6878 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1896 2.7713 1.0769 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8537 1.8120 0.2261 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8017 1.2678 -0.6313 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5104 0.2717 -1.5336 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2158 -0.1959 -1.5761 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2049 -1.1702 -2.5489 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4864 -1.2535 -3.0542 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2351 -0.3792 -2.4244 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0034 -2.8837 0.7396 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6423 -2.6660 2.1765 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4039 -3.4743 0.5926 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1350 -3.8765 0.2479 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7928 3.6801 -1.7179 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5086 3.4822 0.0351 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9624 2.7011 -0.7877 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0596 1.4047 -2.1753 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8067 2.8424 1.0182 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3243 1.9676 1.3906 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7067 1.1876 1.8142 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9149 -1.9949 -1.1781 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3415 -2.0819 -0.1353 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7743 -0.9505 1.1068 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6033 1.4359 0.9190 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2021 3.2459 2.5358 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8214 1.6576 -0.5762 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3324 -1.7311 -2.8238 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7825 -1.9368 -3.8364 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1850 -1.7948 2.5940 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4462 -2.5967 2.2660 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9433 -3.5931 2.7310 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3783 -4.5874 0.7211 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0569 -3.1025 1.4149 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8176 -3.2947 -0.4087 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2594 -3.8580 -0.7460 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 0 3 5 1 0 5 6 2 0 5 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 15 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 8 25 1 0 25 26 1 0 25 27 1 0 25 28 1 0 21 11 1 0 18 12 1 0 24 20 1 0 1 29 1 0 1 30 1 0 1 31 1 0 2 32 1 0 4 33 1 0 4 34 1 0 4 35 1 0 8 36 1 6 9 37 1 0 9 38 1 0 13 39 1 0 14 40 1 0 19 41 1 0 22 42 1 0 23 43 1 0 26 44 1 0 26 45 1 0 26 46 1 0 27 47 1 0 27 48 1 0 27 49 1 0 28 50 1 0 M END

Standard InCHIKey	WXULKGXQMWVWMP-QGZVFWFLSA-N
Standard InCHI	InChI=1S/C21H22O7/c1-5-12(2)20(23)28-17(21(3,4)24)11-26-19-13-6-7-18(22)27-16(13)10-15-14(19)8-9-25-15/h5-10,17,24H,11H2,1-4H3/t17-/m1/s1
SMILES	CC=C(C)C(=O)O[C@H](COc1c2ccc(=O)oc2cc2c1cco2)C(C)(C)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	386.14	Volume:	386.543 ? Van der Waals volume.
Dense:	0.999	LogP:	3.304 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.96 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.633 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	18.0
TPSA:	99.11 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	1.0	Rings:	3.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.393	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.565	Fsp³:	0.333
MCE-18:	42.0 ? 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:	0	PAINS Alert:	0
Colloidal aggregators:	0.245	Fluc inhibitor:	0.745 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.9 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.202 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.084	Promiscuous compounds:	0.116

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.792	MDCK Permeability:	-4.532
Pgp-inhibitor:	0.132	Pgp-substrate:	0.003
PAMPA:	0.232 ? 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):	0.001
20% Bioavailability (F20%):	0.866	30% Bioavailability (F30%):	0.802
50% Bioavailability (F50%):	0.392

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.982
Plasma Protein Binding (PPB):	77.345%	Volume Distribution (VD):	-0.372
Fu:	14.422% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.995
OATP1B3 inhibitor:	0.998	BCRP inhibitor:	0.0
BSEP inhibitor:	0.992

ADMET: Metabolism

CYP1A2-inhibitor:	1.0	CYP1A2-substrate:	0.751
CYP2C19-inhibitor:	0.97	CYP2C19-substrate:	0.014
CYP2C9-inhibitor:	0.987	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.198	CYP2D6-substrate:	0.956
CYP3A4-inhibitor:	0.416	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.003	CYP2C8-inhibitor:	0.965
HLM stability:	0.447 ? 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):

6.201

Half-life (T1/2):

0.63

ADMET: Toxicity

hERG Blockers:	0.095	hERG Blockers (10um):	0.202
Human Hepatotoxicity (H-HT):	0.535	Drug-induced Liver Injury (DILI):	0.902
AMES Toxicity:	0.828	Rat Oral Acute Toxicity:	0.516
Maximum Recommended Daily Dose:	0.757	Skin Sensitization:	0.7
Carcinogencity:	0.918	Eye Corrosion:	0.001
Eye Irritation:	0.442	Respiratory Toxicity:	0.353
Drug-induced Neurotoxicity:	0.165	Ototoxicity:	0.377
Hematotoxicity:	0.318	Drug-induced Nephrotoxicity:	0.702
Genotoxicity:	0.992	RPMI-8226 Immunitoxicity:	0.093
A549 Cytotoxicity:	0.101	Hek293 Cytotoxicity:	0.47
BCF:	1.171 ? 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:	3.866 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.072 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.702 ? 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
NPO662	Angelica officinalis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO662	Angelica officinalis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO662	Angelica officinalis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO662	Angelica officinalis	Species	Apiaceae	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 NPC43644 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	16818
0.1-0.2	31849
0.2-0.3	1045
0.3-0.4	111
0.4-0.5	20
0.5-0.6	7
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
0.6667	Remote Similarity	NPC278010
0.6667	Remote Similarity	NPC250769
0.6667	Remote Similarity	NPC295608
0.6567	Remote Similarity	NPC303210
0.6567	Remote Similarity	NPC95472
0.6567	Remote Similarity	NPC239270
0.6324	Remote Similarity	NPC169
0.6197	Remote Similarity	NPC190970
0.6176	Remote Similarity	NPC88445
0.5789	Remote Similarity	NPC53917
0.5769	Remote Similarity	NPC49009
0.5641	Remote Similarity	NPC269495
0.5625	Remote Similarity	NPC14822
0.5538	Remote Similarity	NPC74539
0.5455	Remote Similarity	NPC191104
0.51	Remote Similarity	NPC325176

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC43644 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4267
0.1-0.2	4822
0.2-0.3	59
0.3-0.4	1
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
0.5538	Remote Similarity	NPD920	Phase 4

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