NPASS Compound

Structure

NPC86150 OpenBabel06302216122D 32 35 0 0 1 0 0 0 0 0999 V2000 -0.9659 0.7412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1305 1.9914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2942 0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 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 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 30 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 26 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 7 32 1 6 0 0 0 8 9 1 6 0 0 0 8 26 1 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 22 1 0 0 0 0 12 13 1 0 0 0 0 12 25 1 6 0 0 0 13 14 1 0 0 0 0 15 14 1 6 0 0 0 15 16 1 0 0 0 0 15 22 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 16 19 1 0 0 0 0 19 20 1 0 0 0 0 19 24 1 1 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 6 0 0 0 26 27 1 6 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	450.37
Volume:	493.779
LogP:	4.204
LogD:	4.153
LogS:	-4.672
# Rotatable Bonds:	3
TPSA:	80.92
# H-Bond Aceptor:	4
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.492
Synthetic Accessibility Score:	4.781
Fsp3:	1.0
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:	-5.075
MDCK Permeability:	7.0613141360809095e-06
Pgp-inhibitor:	0.965
Pgp-substrate:	0.954
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.868
30% Bioavailability (F30%):	0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.021
Plasma Protein Binding (PPB):	89.32638549804688%
Volume Distribution (VD):	0.916
Pgp-substrate:	4.777982234954834%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.292
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.852
CYP2C9-inhibitor:	0.109
CYP2C9-substrate:	0.771
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.457
CYP3A4-inhibitor:	0.056
CYP3A4-substrate:	0.249

ADMET: Excretion

Clearance (CL):	4.914
Half-life (T1/2):	0.098

ADMET: Toxicity

hERG Blockers:	0.034
Human Hepatotoxicity (H-HT):	0.335
Drug-inuced Liver Injury (DILI):	0.012
AMES Toxicity:	0.022
Rat Oral Acute Toxicity:	0.567
Maximum Recommended Daily Dose:	0.866
Skin Sensitization:	0.397
Carcinogencity:	0.003
Eye Corrosion:	0.827
Eye Irritation:	0.163
Respiratory Toxicity:	0.957

Download Data

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

Natural Product: NPC86150

Natural Product ID:	NPC86150
*Common Name:**	AGTWEFWCYVDEIC-CTUPTTDZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	AGTWEFWCYVDEIC-CTUPTTDZSA-N
Standard InCHI:	InChI=1S/C28H50O4/c1-25(2)21-11-9-19(29)17(27(21,5)15-13-23(25)31)7-8-18-20(30)10-12-22-26(3,4)24(32)14-16-28(18,22)6/h17-24,29-32H,7-16H2,1-6H3/t17-,18-,19-,20-,21-,22-,23+,24+,27+,28+/m0/s1
SMILES:	CC1(C)[C@@H]2CC[C@@H]([C@H](CC[C@H]3[C@H](CC[C@H]4C(C)(C)[C@@H](CC[C@]34C)O)O)[C@@]2(C)CC[C@H]1O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11633800
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000129] Alcohols and polyols [CHEMONTID:0001292] Cyclic 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
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/S0031-9422(98)00552-4]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12932142]
NPO24855	Callicarpa americana	Species	Lamiaceae	Eukaryota	fruiting branches	n.a.	n.a.	PMID[17279798]
NPO24671	Lycopodium japonicum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19245240]
NPO24671	Lycopodium japonicum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29460	Petiveria alliacea	Species	Petiveriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27912	Cocculus laurifolius	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24671	Lycopodium japonicum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29277	Lycopodium obscurum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27912	Cocculus laurifolius	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29460	Petiveria alliacea	Species	Petiveriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24671	Lycopodium japonicum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27912	Cocculus laurifolius	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21044	Sphaerellopsis filum	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29087	Ligularia brachyphylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26662	Chrysanthemum foeniculaceum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27361	Hylobius abietis	Species	Curculionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29261	Bryothamnion triquetrum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26989	Delphinium geyeri	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24978	Psila boliviensis	Species	Psilidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26775	Shorea wangtianshuea	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29522	Cuscuta salina	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29277	Lycopodium obscurum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24542	Doris obsoleta	Species	Dorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24671	Lycopodium japonicum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29460	Petiveria alliacea	Species	Petiveriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27912	Cocculus laurifolius	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28418	Grateloupia filicina	Species	Halymeniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29521	Genista purgans	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27937	Centaurea iberica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29247	Wahlenbergia marginata	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18357	Euphorbia sanctae-catharinae	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24855	Callicarpa americana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26339	Dillenia philippinensis	Species	Dilleniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27125	Hovea linearis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24225	Alexandrium peruvianum	Species	Gonyaulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24832	Eriocaulon ligulatum	Species	Eriocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26498	Vernonia cumingiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25798	Gunnera perpensa	Species	Gunneraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28055	Perymenium berlandieri	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22646	Malouetia tamaquarina	Species	Apocynaceae	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 NPC86150 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	477
0.1-0.2	4585
0.2-0.3	17582
0.3-0.4	9267
0.4-0.5	4532
0.5-0.6	4174
0.6-0.7	1632
0.7-0.8	402
0.8-0.85	33
0.85-0.9	13
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 NPC86150 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	498
0.1-0.2	4330
0.2-0.3	3086
0.3-0.4	773
0.4-0.5	261
0.5-0.6	151
0.6-0.7	35
0.7-0.8	16
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