NPASS Compound

Structure

NPC276761 OpenBabel06302215342D 29 32 0 0 1 0 0 0 0 0999 V2000 -0.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3198 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2709 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1369 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0029 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8690 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7350 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7350 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6010 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8690 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0029 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1369 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2709 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3198 1.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 18 1 0 0 0 0 4 2 1 6 0 0 0 4 5 1 0 0 0 0 4 17 1 0 0 0 0 5 6 1 0 0 0 0 6 16 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 14 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 19 18 1 6 0 0 0 19 20 1 0 0 0 0 19 26 1 0 0 0 0 20 21 1 0 0 0 0 20 29 1 1 0 0 0 21 22 1 0 0 0 0 21 28 1 6 0 0 0 22 23 1 0 0 0 0 22 27 1 1 0 0 0 23 24 1 6 0 0 0 23 26 1 0 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	408.14
Volume:	386.18
LogP:	0.944
LogD:	0.501
LogS:	-3.231
# Rotatable Bonds:	4
TPSA:	138.82
# H-Bond Aceptor:	9
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.502
Synthetic Accessibility Score:	4.312
Fsp3:	0.55
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.434
MDCK Permeability:	5.1760995120275766e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.882
Human Intestinal Absorption (HIA):	0.037
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.967

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.138
Plasma Protein Binding (PPB):	62.86353302001953%
Volume Distribution (VD):	0.63
Pgp-substrate:	24.6826229095459%

ADMET: Metabolism

CYP1A2-inhibitor:	0.058
CYP1A2-substrate:	0.097
CYP2C19-inhibitor:	0.023
CYP2C19-substrate:	0.254
CYP2C9-inhibitor:	0.008
CYP2C9-substrate:	0.184
CYP2D6-inhibitor:	0.039
CYP2D6-substrate:	0.473
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.111

ADMET: Excretion

Clearance (CL):	3.919
Half-life (T1/2):	0.5

ADMET: Toxicity

hERG Blockers:	0.154
Human Hepatotoxicity (H-HT):	0.218
Drug-inuced Liver Injury (DILI):	0.514
AMES Toxicity:	0.386
Rat Oral Acute Toxicity:	0.178
Maximum Recommended Daily Dose:	0.057
Skin Sensitization:	0.183
Carcinogencity:	0.816
Eye Corrosion:	0.003
Eye Irritation:	0.036
Respiratory Toxicity:	0.053

Download Data

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

Natural Product: NPC276761

Natural Product ID:	NPC276761
*Common Name:**	HXCGUCZXPFBNRD-NEDVQNLSSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HXCGUCZXPFBNRD-NEDVQNLSSA-N
Standard InCHI:	InChI=1S/C20H24O9/c1-20(2,29-19-18(25)17(24)16(23)13(8-21)28-19)14-6-10-5-9-3-4-15(22)27-11(9)7-12(10)26-14/h3-5,7,13-14,16-19,21,23-25H,6,8H2,1-2H3/t13-,14+,16-,17+,18-,19+/m1/s1
SMILES:	CC(C)([C@@H]1Cc2cc3ccc(=O)oc3cc2O1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	216283
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

*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
NPO24758	Angelica dahurica	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	DOI[10.5012/bkcs.2003.24.11.1699]
NPO15544	Cnidium monnieri	Species	Apiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[10785419]
NPO24758	Angelica dahurica	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[12510838]
NPO3854	Ruta graveolens	Species	Rutaceae	Eukaryota	leaves	n.a.	n.a.	PMID[12568545]
NPO24758	Angelica dahurica	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[15646793]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[17238120]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[18405608]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[18661821]
NPO5045	Aegle marmelos	Species	Rutaceae	Eukaryota	leaves	n.a.	n.a.	PMID[18760601]
NPO3854	Ruta graveolens	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19191562]
NPO30526	0topterygium incisum	n.a.	n.a.	n.a.	n.a.	root	n.a.	PMID[20707067]
NPO30526	0topterygium incisum	n.a.	n.a.	n.a.	n.a.	rhizome	n.a.	PMID[20707067]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21417376]
NPO24758	Angelica dahurica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21625478]
NPO15544	Cnidium monnieri	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21625478]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21627108]
NPO24758	Angelica dahurica	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[21657081]
NPO5045	Aegle marmelos	Species	Rutaceae	Eukaryota	n.a.	bark	n.a.	PMID[21875114]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[22784551]
NPO15544	Cnidium monnieri	Species	Apiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[22932311]
NPO5045	Aegle marmelos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23434131]
NPO15544	Cnidium monnieri	Species	Apiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[23721280]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24813739]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[25068578]
NPO2392	Hansenia weberbaueriana	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25333853]
NPO5045	Aegle marmelos	Species	Rutaceae	Eukaryota	n.a.	fruit	n.a.	PMID[26247834]
NPO24758.1	Angelica dahurica var. formosana	Varieties	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[26552172]
NPO24758	Angelica dahurica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27444348]
NPO3854	Ruta graveolens	Species	Rutaceae	Eukaryota	Whole Plants	n.a.	n.a.	PMID[28093914]
NPO5045	Aegle marmelos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30579794]
NPO24758	Angelica dahurica	Species	Apiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31464439]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[7700984]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30526	0topterygium incisum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO5045	Aegle marmelos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4340	Peucedanum praeruptorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15544	Cnidium monnieri	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3854	Ruta graveolens	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17866	Peucedanum rubricaule	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24758	Angelica dahurica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12746	Pleurospermum rivulorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15544	Cnidium monnieri	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17866	Peucedanum rubricaule	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3854	Ruta graveolens	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2392	Hansenia weberbaueriana	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11302	Hymenidium lindleyanum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12746	Pleurospermum rivulorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4340	Peucedanum praeruptorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5045	Aegle marmelos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24758	Angelica dahurica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5045	Aegle marmelos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4340	Peucedanum praeruptorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24758	Angelica dahurica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3854	Ruta graveolens	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30526	0topterygium incisum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17866	Peucedanum rubricaule	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2392	Hansenia weberbaueriana	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24758	Angelica dahurica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4340	Peucedanum praeruptorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15544	Cnidium monnieri	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15394	Angelica decursiva	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24758	Angelica dahurica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16614	Zanthoxylum spinosum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15544	Cnidium monnieri	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4340	Peucedanum praeruptorum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22273	Angelica pubescens	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	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 NPC276761 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	370
0.1-0.2	1495
0.2-0.3	3338
0.3-0.4	7778
0.4-0.5	10444
0.5-0.6	5011
0.6-0.7	5666
0.7-0.8	5692
0.8-0.85	2214
0.85-0.9	608
0.9-0.95	76
0.95-1	5

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 NPC276761 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	316
0.1-0.2	884
0.2-0.3	1762
0.3-0.4	2605
0.4-0.5	2037
0.5-0.6	1029
0.6-0.7	328
0.7-0.8	149
0.8-0.85	30
0.85-0.9	10
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