NPASS Compound

Structure

NPC79913 OpenBabel06302215232D 28 32 0 0 1 0 0 0 0 0999 V2000 -0.1212 -2.6664 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5920 -1.8838 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9535 -2.0352 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5183 -0.7872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5058 0.1356 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2255 0.6324 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.2277 1.1589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6222 1.4996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5642 1.4996 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4355 0.5871 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0852 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3153 -0.5421 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3153 -1.2931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.8584 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0768 -1.2078 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0060 -0.5192 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8154 -0.8651 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0683 0.8460 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7424 0.7313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1787 1.2578 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9801 0.0903 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5438 -0.4361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7816 -1.0772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4556 -1.1918 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8919 -0.6654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6542 -0.0244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3639 0.6241 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 12 1 0 0 0 0 5 6 1 0 0 0 0 5 28 1 6 0 0 0 6 16 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 16 1 0 0 0 0 10 11 1 0 0 0 0 10 19 1 1 0 0 0 11 12 1 0 0 0 0 11 18 1 1 0 0 0 12 13 1 6 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 16 17 1 6 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 27 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	386.17
Volume:	385.845
LogP:	2.566
LogD:	1.837
LogS:	-4.427
# Rotatable Bonds:	3
TPSA:	93.06
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.756
Synthetic Accessibility Score:	6.226
Fsp3:	0.636
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.537
MDCK Permeability:	1.7633299648878165e-05
Pgp-inhibitor:	0.007
Pgp-substrate:	0.831
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.903
30% Bioavailability (F30%):	0.388

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.92
Plasma Protein Binding (PPB):	81.26712799072266%
Volume Distribution (VD):	0.602
Pgp-substrate:	16.157320022583008%

ADMET: Metabolism

CYP1A2-inhibitor:	0.097
CYP1A2-substrate:	0.951
CYP2C19-inhibitor:	0.077
CYP2C19-substrate:	0.758
CYP2C9-inhibitor:	0.069
CYP2C9-substrate:	0.031
CYP2D6-inhibitor:	0.013
CYP2D6-substrate:	0.061
CYP3A4-inhibitor:	0.665
CYP3A4-substrate:	0.556

ADMET: Excretion

Clearance (CL):	6.386
Half-life (T1/2):	0.155

ADMET: Toxicity

hERG Blockers:	0.035
Human Hepatotoxicity (H-HT):	0.659
Drug-inuced Liver Injury (DILI):	0.806
AMES Toxicity:	0.234
Rat Oral Acute Toxicity:	0.347
Maximum Recommended Daily Dose:	0.673
Skin Sensitization:	0.848
Carcinogencity:	0.994
Eye Corrosion:	0.004
Eye Irritation:	0.035
Respiratory Toxicity:	0.985

Download Data

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General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC79913

Natural Product ID:	NPC79913
*Common Name:**	BRRTVYWNYBLCAX-AKTXGRJUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BRRTVYWNYBLCAX-AKTXGRJUSA-N
Standard InCHI:	InChI=1S/C22H26O6/c1-13-9-10-21(26)18(2)12-27-22(28-16(24)14-7-5-4-6-8-14)17(25)20(13,21)11-15(23)19(18,22)3/h4-8,13,17,25-26H,9-12H2,1-3H3/t13-,17-,18-,19-,20+,21+,22-/m1/s1
SMILES:	C[C@@H]1CC[C@@]2([C@]3(C)CO[C@]4([C@@H]([C@]12CC(=O)[C@]34C)O)OC(=O)c1ccccc1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0000176] Benzoic acids and derivatives [CHEMONTID:0001350] Benzoic acid esters

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO14260	Euphorbia kansui	Species	Euphorbiaceae	Eukaryota	roots	n.a.	n.a.	PMID[12350140]
NPO14260	Euphorbia kansui	Species	Euphorbiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[12762796]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	bark	n.a.	PMID[15283458]
NPO14260	Euphorbia kansui	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15387657]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	stem	n.a.	PMID[15577257]
NPO14260	Euphorbia kansui	Species	Euphorbiaceae	Eukaryota	n.a.	root	n.a.	PMID[1955882]
NPO8896	Anacardium occidentale	Species	Anacardiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[8021657]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9051910]
NPO8896	Anacardium occidentale	Species	Anacardiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO13274	Illicium verum	Species	Schisandraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO8896	Anacardium occidentale	Species	Anacardiaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO8896	Anacardium occidentale	Species	Anacardiaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO13274	Illicium verum	Species	Schisandraceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO13274	Illicium verum	Species	Schisandraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO8896	Anacardium occidentale	Species	Anacardiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO8896	Anacardium occidentale	Species	Anacardiaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO13274	Illicium verum	Species	Schisandraceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO5911	Anchusa officinalis	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12693	Mesembryanthemum tortuosum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8896	Anacardium occidentale	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13274	Illicium verum	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14260	Euphorbia kansui	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12693	Mesembryanthemum tortuosum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13274	Illicium verum	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5911	Anchusa officinalis	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14260	Euphorbia kansui	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8896	Anacardium occidentale	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13274	Illicium verum	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14260	Euphorbia kansui	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8896	Anacardium occidentale	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14260	Euphorbia kansui	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13274	Illicium verum	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13274	Illicium verum	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5911	Anchusa officinalis	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14260	Euphorbia kansui	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13970	Caryopteris mongholica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10551	Acanthopanax ricinifolius	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO14465	Ramalina terebrata	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12693	Mesembryanthemum tortuosum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18379	Satureja atropatana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16137	Mappia foetida	Species	Icacinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8896	Anacardium occidentale	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7027	Metapenaeus macleayi	Species	Penaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16626	Leucetta microrhaphis	Species	Leucettidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6519	Calocera viscosa	Species	Dacrymycetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13368	Monomorium delagoense	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10773	Dalbergia rubiginosa	Species	Fabaceae	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	NP ID	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC79913 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	353
0.1-0.2	1225
0.2-0.3	2619
0.3-0.4	4877
0.4-0.5	9340
0.5-0.6	12306
0.6-0.7	9978
0.7-0.8	1545
0.8-0.85	251
0.85-0.9	199
0.9-0.95	4
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC79913 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	289
0.1-0.2	765
0.2-0.3	1740
0.3-0.4	2996
0.4-0.5	2193
0.5-0.6	886
0.6-0.7	243
0.7-0.8	36
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

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