NPASS Compound

Structure

NPC71375 OpenBabel06302215552D 24 28 0 0 1 0 0 0 0 0999 V2000 1.7601 0.2788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9511 -1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5388 -2.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -2.9271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.6180 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -3.1180 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -4.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -4.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -4.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -4.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -4.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -4.6180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -3.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.1180 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5640 -3.3769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.6180 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.6180 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 0.9511 0.0000 C 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 23 1 0 0 0 0 3 4 1 1 0 0 0 3 21 1 0 0 0 0 4 5 1 0 0 0 0 6 5 1 6 0 0 0 6 7 1 0 0 0 0 6 21 1 0 0 0 0 7 8 1 6 0 0 0 7 18 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 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 1 1 0 0 0 16 18 1 0 0 0 0 18 19 1 1 0 0 0 19 20 1 0 0 0 0 21 20 1 1 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	325.24
Volume:	358.163
LogP:	4.692
LogD:	4.07
LogS:	-4.129
# Rotatable Bonds:	0
TPSA:	20.31
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.621
Synthetic Accessibility Score:	5.089
Fsp3:	0.773
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.703
MDCK Permeability:	1.0693936928873882e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.098
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.015
30% Bioavailability (F30%):	0.961

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.222
Plasma Protein Binding (PPB):	71.73766326904297%
Volume Distribution (VD):	0.972
Pgp-substrate:	16.515029907226562%

ADMET: Metabolism

CYP1A2-inhibitor:	0.046
CYP1A2-substrate:	0.281
CYP2C19-inhibitor:	0.064
CYP2C19-substrate:	0.901
CYP2C9-inhibitor:	0.074
CYP2C9-substrate:	0.074
CYP2D6-inhibitor:	0.723
CYP2D6-substrate:	0.168
CYP3A4-inhibitor:	0.929
CYP3A4-substrate:	0.87

ADMET: Excretion

Clearance (CL):	18.881
Half-life (T1/2):	0.258

ADMET: Toxicity

hERG Blockers:	0.04
Human Hepatotoxicity (H-HT):	0.505
Drug-inuced Liver Injury (DILI):	0.737
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.76
Maximum Recommended Daily Dose:	0.893
Skin Sensitization:	0.955
Carcinogencity:	0.742
Eye Corrosion:	0.225
Eye Irritation:	0.03
Respiratory Toxicity:	0.989

Download Data

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

Natural Product: NPC71375

Natural Product ID:	NPC71375
*Common Name:**	PSOQPSXOOXHHBU-NJAOXFEXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PSOQPSXOOXHHBU-NJAOXFEXSA-N
Standard InCHI:	InChI=1S/C22H31NO/c1-14-18-6-7-20-17-5-4-15-12-16(24)8-10-21(15,2)19(17)9-11-22(18,20)13-23(14)3/h8,10,12,14,17-20H,4-7,9,11,13H2,1-3H3/t14-,17+,18+,19-,20+,21-,22+/m0/s1
SMILES:	C[C@H]1[C@H]2CC[C@@H]3[C@@H]4CCC5=CC(=O)C=C[C@]5(C)[C@H]4CC[C@@]23CN1C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002724] Steroidal alkaloids [CHEMONTID:0002731] Conanine-type alkaloids

*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
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1007/s11418-005-0009-z]
NPO27885	Aspergillus nidulans	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11251292]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[17489632]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	stem	n.a.	PMID[18484536]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	stem bark	Mukono, Uganda	2005-JUN	PMID[19008110]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19836230]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20337486]
NPO2713	Xylopia caudata	Species	Annonaceae	Eukaryota	Trunk bark	the dense rainy forest of Jelebu, in Negeri Sembilan state, Malaysia	2006-FEB	PMID[20481544]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21116437]
NPO27885	Aspergillus nidulans	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22026385]
NPO522	Oenanthe javanica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31125231]
NPO27885	Aspergillus nidulans	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6875511]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO522	Oenanthe javanica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9530	Scrophularia nodosa	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9530	Scrophularia nodosa	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO522	Oenanthe javanica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9530	Scrophularia nodosa	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO522	Oenanthe javanica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9530	Scrophularia nodosa	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO522	Oenanthe javanica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2713	Xylopia caudata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27885	Aspergillus nidulans	Species	Aspergillaceae	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 NPC71375 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	109
0.1-0.2	1307
0.2-0.3	17284
0.3-0.4	13678
0.4-0.5	7846
0.5-0.6	2188
0.6-0.7	229
0.7-0.8	54
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
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 NPC71375 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	101
0.1-0.2	695
0.2-0.3	4273
0.3-0.4	3029
0.4-0.5	782
0.5-0.6	239
0.6-0.7	28
0.7-0.8	3
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