NPASS Compound

Structure

NPC90973 OpenBabel06302215522D 25 29 0 0 1 0 0 0 0 0999 V2000 -1.3538 -1.3954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8394 -0.4916 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3138 -1.3889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6847 -0.0104 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5241 -0.5020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3695 -0.0208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3755 0.9519 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2384 0.4465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5361 1.4434 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5428 2.3941 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3757 2.8749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2088 3.3559 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0481 2.8644 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8748 3.3339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6948 2.8528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6881 1.9021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8614 1.4326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0415 1.9137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2084 1.4327 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.6908 0.9623 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6972 2.0022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8514 1.4538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0060 0.9727 0.0000 C 0 0 0 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 0.9038 -0.5144 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 24 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 6 0 0 0 4 20 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 19 1 0 0 0 0 7 8 1 1 0 0 0 7 9 1 0 0 0 0 9 10 1 6 0 0 0 9 20 1 0 0 0 0 10 11 1 0 0 0 0 11 19 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 18 2 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 2 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 20 21 1 6 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	335.22
Volume:	370.187
LogP:	4.894
LogD:	4.162
LogS:	-4.863
# Rotatable Bonds:	0
TPSA:	22.0
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.637
Synthetic Accessibility Score:	4.201
Fsp3:	0.609
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:	-5.038
MDCK Permeability:	2.650940223247744e-05
Pgp-inhibitor:	0.903
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.306
Plasma Protein Binding (PPB):	94.27299499511719%
Volume Distribution (VD):	0.907
Pgp-substrate:	4.04404354095459%

ADMET: Metabolism

CYP1A2-inhibitor:	0.282
CYP1A2-substrate:	0.687
CYP2C19-inhibitor:	0.756
CYP2C19-substrate:	0.943
CYP2C9-inhibitor:	0.622
CYP2C9-substrate:	0.803
CYP2D6-inhibitor:	0.219
CYP2D6-substrate:	0.254
CYP3A4-inhibitor:	0.835
CYP3A4-substrate:	0.801

ADMET: Excretion

Clearance (CL):	15.401
Half-life (T1/2):	0.384

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.314
Drug-inuced Liver Injury (DILI):	0.045
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.126
Maximum Recommended Daily Dose:	0.959
Skin Sensitization:	0.071
Carcinogencity:	0.079
Eye Corrosion:	0.003
Eye Irritation:	0.068
Respiratory Toxicity:	0.951

Download Data

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

Natural Product: NPC90973

Natural Product ID:	NPC90973
*Common Name:**	NEPLKJAINOWIJL-YDLSIGKMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NEPLKJAINOWIJL-YDLSIGKMSA-N
Standard InCHI:	InChI=1S/C23H29NO/c1-21(2)18-9-12-23(4)19(22(18,3)11-10-20(21)25)14-16-13-15-7-5-6-8-17(15)24(16)23/h5-8,13,18-19H,9-12,14H2,1-4H3/t18-,19+,22-,23-/m0/s1
SMILES:	CC1(C)[C@@H]2CC[C@@]3(C)[C@H](Cc4cc5ccccc5n34)[C@@]2(C)CCC1=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000211] Indoles and derivatives [CHEMONTID:0002497] Indoles

*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
NPO4501	Caragana intermedia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15620236]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO16473	Araucaria bidwillii	Species	Araucariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23170	Orobanche coerulescens	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23170	Orobanche coerulescens	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16473	Araucaria bidwillii	Species	Araucariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23170	Orobanche coerulescens	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23170	Orobanche coerulescens	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14893	Streptomyces eurocidicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO28729	Spirostachys africana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24723	Ophiorrhiza bracteata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23170	Orobanche coerulescens	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21816	Calea jamaicensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25164	Polyalthia suaveolens	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24593	Campanula pyramidalis	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16473	Araucaria bidwillii	Species	Araucariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24561	Sesuvium portulacastrum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25009	Cystoseira myrica	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4501	Caragana intermedia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24939	Veronica officinalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13718	Poria tenuis	Species	Coccinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12599.1	Pinus leiophylla var. chihuahuana	Varieties	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24123	Ramalina scopulorum	Species	Ramalinaceae	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 NPC90973 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	530
0.1-0.2	2241
0.2-0.3	10717
0.3-0.4	21497
0.4-0.5	3815
0.5-0.6	2416
0.6-0.7	1254
0.7-0.8	223
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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 NPC90973 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	332
0.1-0.2	594
0.2-0.3	735
0.3-0.4	2176
0.4-0.5	2653
0.5-0.6	1997
0.6-0.7	610
0.7-0.8	53
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