NPASS Compound

Structure

NPC124385 OpenBabel06302215342D 29 32 0 0 1 0 0 0 0 0999 V2000 0.0014 -1.9424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8422 -1.4567 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8419 -0.4857 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6824 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6821 0.9719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9714 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0006 1.9714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8422 1.4571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8425 2.4291 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6844 2.9148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5260 2.4286 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3673 2.9143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3676 3.9143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2334 3.4143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2084 2.4281 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2081 1.4561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3668 0.9704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5257 1.4566 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5255 0.4566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6838 0.9709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6836 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8416 -0.4862 0.0000 C 0 0 2 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 0.0003 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8414 -1.4862 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0746 2.9277 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6832 -1.9420 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5240 -1.4562 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6835 -2.9129 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 27 1 0 0 0 0 3 2 1 6 0 0 0 3 4 1 0 0 0 0 3 23 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 23 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 20 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 18 1 0 0 0 0 12 13 1 0 0 0 0 12 14 1 0 0 0 0 12 15 1 0 0 0 0 15 16 1 0 0 0 0 15 26 1 6 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 18 20 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 25 1 6 0 0 0 23 24 1 6 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	276.14
Volume:	281.305
LogP:	5.73
LogD:	4.993
LogS:	-5.572
# Rotatable Bonds:	1
TPSA:	0.0
# H-Bond Aceptor:	0
# H-Bond Donor:	0
# Rings:	2
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.558
Synthetic Accessibility Score:	4.626
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.444
MDCK Permeability:	2.1501677110791206e-05
Pgp-inhibitor:	0.91
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.707
30% Bioavailability (F30%):	0.853

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.222
Plasma Protein Binding (PPB):	97.96405792236328%
Volume Distribution (VD):	2.531
Pgp-substrate:	2.038365602493286%

ADMET: Metabolism

CYP1A2-inhibitor:	0.504
CYP1A2-substrate:	0.738
CYP2C19-inhibitor:	0.348
CYP2C19-substrate:	0.94
CYP2C9-inhibitor:	0.506
CYP2C9-substrate:	0.117
CYP2D6-inhibitor:	0.303
CYP2D6-substrate:	0.088
CYP3A4-inhibitor:	0.901
CYP3A4-substrate:	0.853

ADMET: Excretion

Clearance (CL):	11.458
Half-life (T1/2):	0.121

ADMET: Toxicity

hERG Blockers:	0.199
Human Hepatotoxicity (H-HT):	0.054
Drug-inuced Liver Injury (DILI):	0.633
AMES Toxicity:	0.043
Rat Oral Acute Toxicity:	0.097
Maximum Recommended Daily Dose:	0.042
Skin Sensitization:	0.857
Carcinogencity:	0.352
Eye Corrosion:	0.973
Eye Irritation:	0.786
Respiratory Toxicity:	0.625

Download Data

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

Natural Product: NPC124385

Natural Product ID:	NPC124385
*Common Name:**	BRPIABZRYYNFFV-MUNARKKMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BRPIABZRYYNFFV-MUNARKKMSA-N
Standard InCHI:	InChI=1S/C25H38O4/c1-14(21(28)29)15-9-12-24(5)16-7-8-18-22(2,3)19(26)10-11-23(18,4)17(16)13-20(27)25(15,24)6/h7,13-15,18-20,26-27H,8-12H2,1-6H3,(H,28,29)/t14-,15+,18-,19-,20+,23+,24-,25-/m0/s1
SMILES:	C[C@@H]([C@H]1CC[C@@]2(C)C3=CC[C@H]4C(C)(C)[C@H](CC[C@]4(C)C3=C[C@H]([C@]12C)O)O)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101290463
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001445] Bile acids, alcohols and derivatives [CHEMONTID:0002194] Hydroxy bile acids, alcohols and derivatives [CHEMONTID:0000516] Dihydroxy bile acids, alcohols and derivatives

*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
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	callus	n.a.	PMID[10552648]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[18214349]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	seed	n.a.	PMID[21049975]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21800857]
NPO8234	Vernonia galamensis	Species	Asteraceae	Eukaryota	n.a.	seed	n.a.	PMID[9930408]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO9455	Uncaria orientalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO8620	Caesalpinia major	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9455	Uncaria orientalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24536	Senecio cylindricus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5954	Petroselinum crispum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9330	Odinia antillensis	Species	Odiniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2389	Pinus japonica	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3668	Kalanchoe delagoensis	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8234	Vernonia galamensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4875	Ugni molinae	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4072	Anacyclus radiatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8771	Heterodermia dissecta	Species	Physciaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7188	Zieria granulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9072	Bolocera tuediae	Species	Actiniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9455	Uncaria orientalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8009	Arctotis venusta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5540	Amorpha canescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6292	Teucrium brevifolium	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5832	Acacia nelsonii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4321	Siphula ceratites	Species	Icmadophilaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8620	Caesalpinia major	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 NPC124385 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	171
0.1-0.2	998
0.2-0.3	4069
0.3-0.4	9660
0.4-0.5	12816
0.5-0.6	6918
0.6-0.7	5909
0.7-0.8	1868
0.8-0.85	214
0.85-0.9	67
0.9-0.95	7
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 NPC124385 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	149
0.1-0.2	1322
0.2-0.3	3766
0.3-0.4	2564
0.4-0.5	828
0.5-0.6	217
0.6-0.7	212
0.7-0.8	92
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

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