NPASS Compound

Structure

NPC292988 OpenBabel06302216142D 27 31 0 0 1 0 0 0 0 0999 V2000 -0.3535 -2.2949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0204 -1.4453 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3464 -2.2809 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4799 -1.2280 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3643 -0.7403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4819 0.3878 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7006 1.3068 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1319 2.1110 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1076 1.0319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5249 1.6896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5468 -0.2461 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2457 -0.6986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2609 -0.1716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8162 0.0851 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8162 0.5986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0605 1.1048 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2609 0.8553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7056 0.5986 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5823 1.1048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4590 0.5986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3357 1.1048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3357 2.1171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4590 2.6233 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5823 2.1171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7056 0.0851 0.0000 O 0 0 0 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 -0.3321 0.8500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 11 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 1 0 0 0 4 26 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 26 1 0 0 0 0 7 8 1 6 0 0 0 7 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 25 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 26 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 18 25 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 26 27 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	288.06
Volume:	276.613
LogP:	1.858
LogD:	1.521
LogS:	-3.865
# Rotatable Bonds:	1
TPSA:	107.22
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.599
Synthetic Accessibility Score:	3.053
Fsp3:	0.133
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.196
MDCK Permeability:	7.843187631806359e-06
Pgp-inhibitor:	0.005
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.016
20% Bioavailability (F20%):	0.852
30% Bioavailability (F30%):	0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.022
Plasma Protein Binding (PPB):	95.03064727783203%
Volume Distribution (VD):	0.449
Pgp-substrate:	4.862152576446533%

ADMET: Metabolism

CYP1A2-inhibitor:	0.466
CYP1A2-substrate:	0.128
CYP2C19-inhibitor:	0.238
CYP2C19-substrate:	0.053
CYP2C9-inhibitor:	0.728
CYP2C9-substrate:	0.669
CYP2D6-inhibitor:	0.339
CYP2D6-substrate:	0.303
CYP3A4-inhibitor:	0.298
CYP3A4-substrate:	0.172

ADMET: Excretion

Clearance (CL):	19.633
Half-life (T1/2):	0.901

ADMET: Toxicity

hERG Blockers:	0.046
Human Hepatotoxicity (H-HT):	0.095
Drug-inuced Liver Injury (DILI):	0.913
AMES Toxicity:	0.476
Rat Oral Acute Toxicity:	0.739
Maximum Recommended Daily Dose:	0.149
Skin Sensitization:	0.954
Carcinogencity:	0.628
Eye Corrosion:	0.004
Eye Irritation:	0.929
Respiratory Toxicity:	0.181

Download Data

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

Natural Product: NPC292988

Natural Product ID:	NPC292988
*Common Name:**	NZANVYUIDHOMEY-VTKNXMALSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NZANVYUIDHOMEY-VTKNXMALSA-N
Standard InCHI:	InChI=1S/C22H24O5/c1-19(2)15-11-26-21(4)18(24)20(19,3)17-16(22(15,21)25)13(23)10-14(27-17)12-8-6-5-7-9-12/h5-9,14-15,25H,10-11H2,1-4H3/t14-,15-,20+,21+,22+/m0/s1
SMILES:	CC1(C)[C@@H]2CO[C@]3(C)C(=O)[C@@]1(C)C1=C(C(=O)C[C@@H](c4ccccc4)O1)[C@]23O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101324818
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001729] Oxepanes

*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
NPO16533	Erythrophleum fordii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24332631]
NPO29007	Brassica juncea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25700090]
NPO19800	Calophyllum teysmannii	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8792623]
NPO19800	Calophyllum teysmannii	Species	Calophyllaceae	Eukaryota	n.a.	latex	n.a.	PMID[8864237]
NPO29007	Brassica juncea	Species	Brassicaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO29007	Brassica juncea	Species	Brassicaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO29007	Brassica juncea	Species	Brassicaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO19800	Calophyllum teysmannii	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29007	Brassica juncea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19800	Calophyllum teysmannii	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29007	Brassica juncea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29007	Brassica juncea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29007	Brassica juncea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19992	Rubus medius	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19800	Calophyllum teysmannii	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16533	Erythrophleum fordii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20878	Graphis desquamescens	Species	Aclididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19386	Monactis macbridei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5101	Eria bracteata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21304	Vernonia hindei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29007	Brassica juncea	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18127	Lotus arabicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21560	Ascidia ceratodes	Species	Ascidiidae	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 NPC292988 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	347
0.1-0.2	1103
0.2-0.3	2408
0.3-0.4	4651
0.4-0.5	9237
0.5-0.6	11398
0.6-0.7	11611
0.7-0.8	1851
0.8-0.85	89
0.85-0.9	2
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 NPC292988 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	295
0.1-0.2	716
0.2-0.3	1557
0.3-0.4	2890
0.4-0.5	2206
0.5-0.6	1118
0.6-0.7	353
0.7-0.8	15
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