NPASS Compound

Structure

NPC149543 OpenBabel06302216132D 32 36 0 0 1 0 0 0 0 0999 V2000 -0.1546 -1.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8426 -0.4865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7415 -0.8588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6852 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6852 0.9730 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5279 1.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3705 0.9730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2131 1.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2131 2.4324 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0557 2.9189 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0557 1.9459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8983 2.4324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7410 2.9189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7410 3.8919 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.8983 4.3784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4118 5.2210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3848 5.2210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0557 3.8919 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2131 4.3784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3705 3.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3705 2.9189 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6852 3.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5279 2.4324 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5279 3.4054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6852 2.9189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8426 2.4324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8426 1.4595 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 1.9459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9730 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8426 1.4595 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5836 4.3784 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 30 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 27 1 0 0 0 0 6 23 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 21 1 0 0 0 0 10 18 1 0 0 0 0 10 11 1 6 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 32 1 6 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 15 18 1 0 0 0 0 18 19 1 6 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 6 0 0 0 21 23 1 0 0 0 0 23 24 1 1 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 6 0 0 0 27 29 1 0 0 0 0 29 30 1 0 0 0 0 29 31 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	442.38
Volume:	499.598
LogP:	6.493
LogD:	5.28
LogS:	-5.765
# Rotatable Bonds:	0
TPSA:	40.46
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.391
Synthetic Accessibility Score:	4.724
Fsp3:	0.933
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.025
MDCK Permeability:	1.1197864296264015e-05
Pgp-inhibitor:	0.115
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.909
30% Bioavailability (F30%):	0.876

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.403
Plasma Protein Binding (PPB):	95.43688201904297%
Volume Distribution (VD):	1.176
Pgp-substrate:	3.2990996837615967%

ADMET: Metabolism

CYP1A2-inhibitor:	0.026
CYP1A2-substrate:	0.179
CYP2C19-inhibitor:	0.064
CYP2C19-substrate:	0.935
CYP2C9-inhibitor:	0.206
CYP2C9-substrate:	0.489
CYP2D6-inhibitor:	0.031
CYP2D6-substrate:	0.431
CYP3A4-inhibitor:	0.435
CYP3A4-substrate:	0.373

ADMET: Excretion

Clearance (CL):	6.615
Half-life (T1/2):	0.067

ADMET: Toxicity

hERG Blockers:	0.139
Human Hepatotoxicity (H-HT):	0.187
Drug-inuced Liver Injury (DILI):	0.017
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.962
Maximum Recommended Daily Dose:	0.991
Skin Sensitization:	0.59
Carcinogencity:	0.028
Eye Corrosion:	0.088
Eye Irritation:	0.139
Respiratory Toxicity:	0.981

Download Data

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

Natural Product: NPC149543

Natural Product ID:	NPC149543
*Common Name:**	ZEGUWBQDYDXBNS-FVFJQADASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZEGUWBQDYDXBNS-FVFJQADASA-N
Standard InCHI:	InChI=1S/C30H50O2/c1-25(2)17-20-19-9-10-22-28(6)13-12-23(31)26(3,4)21(28)11-14-30(22,8)29(19,7)16-15-27(20,5)24(32)18-25/h9,20-24,31-32H,10-18H2,1-8H3/t20-,21-,22+,23-,24+,27+,28-,29+,30+/m0/s1
SMILES:	CC1(C)C[C@H]2C3=CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]4(C)[C@]3(C)CC[C@@]2(C)[C@@H](C1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	9846221
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	root	n.a.	PMID[11374966]
NPO2280	Streptomyces griseochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[12964155]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16038550]
NPO11789	Swertia decussata	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16286309]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17583950]
NPO733	Pseudoceratina arabica	Species	Pseudoceratinidae	Eukaryota	n.a.	Red Sea	n.a.	PMID[18598078]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18855446]
NPO2280	Streptomyces griseochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19191560]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20455578]
NPO12644	Lunularia cruciata	Species	Lunulariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21625478]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21775156]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23286284]
NPO2280	Streptomyces griseochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23377931]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24108414]
NPO3292	Desmodium styracifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25620156]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27569393]
NPO4734	Syzygium nervosum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27797185]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29185738]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30351923]
NPO12644	Lunularia cruciata	Species	Lunulariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30848895]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	root	n.a.	PMID[3655791]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	roots	n.a.	n.a.	PMID[9834151]
NPO3292	Desmodium styracifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24178	Citrus rugulosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26606	Macadamia ternifolia	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7001	Berberis floribunda	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7319	Jamesoniella colorata	Species	Jungermanniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3292	Desmodium styracifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9452	Pulsatilla campanella	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8701	Bonamia spectabilis	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7001	Berberis floribunda	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24178	Citrus rugulosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26606	Macadamia ternifolia	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3292	Desmodium styracifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3292	Desmodium styracifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26606	Macadamia ternifolia	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11534	Astragalus spinosus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9452	Pulsatilla campanella	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12864	Trogoderma granarium	Species	Dermestidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3311	Diplacus longiflorus	Species	Phrymaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO733	Pseudoceratina arabica	Species	Pseudoceratinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11910	Peltogyne pubescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3658	Achillea pseudopectinata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12644	Lunularia cruciata	Species	Lunulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11223	Pleurotus japonicus	Species	Pleurotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2280	Streptomyces griseochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO18447	Papaver tatricum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12169	Ranunculus peltatus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23899	Rosulabryum capillare	Species	Bryaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6572	Dunalia solanacea	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3292	Desmodium styracifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4910	Lepidosperma ustulatum	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8701	Bonamia spectabilis	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7319	Jamesoniella colorata	Species	Jungermanniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2565	Aglaia australiensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8398	Cymodocea nodosa	Species	Cymodoceaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8006	Berlinia tomentosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7001	Berberis floribunda	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24178	Citrus rugulosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12284	Hydrangea serrata	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9640	Dinophysis fortii	Species	Dinophysiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7627	Fumaria micrantha	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15439	Iyengaria stellata	Species	Scytosiphonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9226	Astragalus pycnanthus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4734	Syzygium nervosum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10546	Allagopappus viscosissimus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7949	Pterodon emarginatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9009	Atuna racemosa	Species	Chrysobalanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11789	Swertia decussata	Species	Gentianaceae	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 NPC149543 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	202
0.1-0.2	1777
0.2-0.3	7632
0.3-0.4	16546
0.4-0.5	6645
0.5-0.6	4819
0.6-0.7	3455
0.7-0.8	1198
0.8-0.85	254
0.85-0.9	125
0.9-0.95	16
0.95-1	28

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 NPC149543 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	189
0.1-0.2	2037
0.2-0.3	4224
0.3-0.4	1935
0.4-0.5	399
0.5-0.6	188
0.6-0.7	158
0.7-0.8	16
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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