NPASS Compound

Structure

NPC83157 OpenBabel06302216182D 32 36 0 0 1 0 0 0 0 0999 V2000 -1.7166 -1.1460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0181 -2.0747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9731 -2.2779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3646 -2.8001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6660 -3.7288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4096 -2.5968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1081 -1.6681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8469 -1.4648 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.5004 -2.1903 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8466 -0.4885 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.6918 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6915 0.9773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9768 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.0006 1.9768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8469 1.4652 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8472 2.4426 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6938 2.9311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5401 2.4421 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -3.3861 2.9306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3864 3.9306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2522 3.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2319 2.4417 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -4.2316 1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3856 0.9758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5398 1.4648 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.5396 0.4873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6932 0.9763 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.6930 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8463 -0.4889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 3 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 -5.0981 2.9413 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 10 30 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 30 1 0 0 0 0 13 14 1 0 0 0 0 13 15 1 0 0 0 0 15 27 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 25 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 19 22 1 0 0 0 0 22 23 1 0 0 0 0 22 32 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 27 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	440.4
Volume:	508.103
LogP:	7.067
LogD:	5.698
LogS:	-6.303
# Rotatable Bonds:	5
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.425
Synthetic Accessibility Score:	5.447
Fsp3:	0.935
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.998
MDCK Permeability:	1.0277648470946588e-05
Pgp-inhibitor:	0.029
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.906
30% Bioavailability (F30%):	0.925

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.567
Plasma Protein Binding (PPB):	99.63823699951172%
Volume Distribution (VD):	1.426
Pgp-substrate:	2.086150884628296%

ADMET: Metabolism

CYP1A2-inhibitor:	0.018
CYP1A2-substrate:	0.479
CYP2C19-inhibitor:	0.064
CYP2C19-substrate:	0.964
CYP2C9-inhibitor:	0.091
CYP2C9-substrate:	0.403
CYP2D6-inhibitor:	0.121
CYP2D6-substrate:	0.857
CYP3A4-inhibitor:	0.338
CYP3A4-substrate:	0.623

ADMET: Excretion

Clearance (CL):	12.451
Half-life (T1/2):	0.008

ADMET: Toxicity

hERG Blockers:	0.028
Human Hepatotoxicity (H-HT):	0.135
Drug-inuced Liver Injury (DILI):	0.024
AMES Toxicity:	0.025
Rat Oral Acute Toxicity:	0.189
Maximum Recommended Daily Dose:	0.665
Skin Sensitization:	0.22
Carcinogencity:	0.017
Eye Corrosion:	0.003
Eye Irritation:	0.194
Respiratory Toxicity:	0.739

Download Data

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

Natural Product: NPC83157

Natural Product ID:	NPC83157
*Common Name:**	BDHQMRXFDYJGII-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BDHQMRXFDYJGII-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C31H52O/c1-20(2)21(3)9-10-22(4)23-13-15-29(8)25-12-11-24-27(5,6)26(32)14-16-30(24)19-31(25,30)18-17-28(23,29)7/h20,22-26,32H,3,9-19H2,1-2,4-8H3
SMILES:	CC(C)C(=C)CCC(C)C1CCC2(C)C3CCC4C(C)(C)C(CCC54CC35CCC12C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	544165
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002321] Cycloartanols 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
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	Brazilian	n.a.	PMID[15387656]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	ripe fruit	n.a.	PMID[16205005]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	fruit	n.a.	PMID[16417304]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	roots	n.a.	n.a.	PMID[16792421]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	branch	n.a.	PMID[17202693]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	whole plants	Panshi, Jilin Province, China	2009-JUN	PMID[21534540]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[21534540]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	roots	n.a.	n.a.	PMID[24660966]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25453801]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26702644]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28383891]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29148766]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31184480]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[33253570]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[3701342]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17458	Sparganium stoloniferum	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17458	Sparganium stoloniferum	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18932.1	Melia azedarach var. toosendan	Varieties	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17458	Sparganium stoloniferum	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18932.1	Melia azedarach var. toosendan	Varieties	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17458	Sparganium stoloniferum	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18932	Melia azedarach	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17458	Sparganium stoloniferum	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18932.1	Melia azedarach var. toosendan	Varieties	Meliaceae	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 NPC83157 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	184
0.1-0.2	2489
0.2-0.3	13754
0.3-0.4	11929
0.4-0.5	5134
0.5-0.6	5315
0.6-0.7	2848
0.7-0.8	840
0.8-0.85	116
0.85-0.9	67
0.9-0.95	10
0.95-1	11

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 NPC83157 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	198
0.1-0.2	2748
0.2-0.3	4377
0.3-0.4	1263
0.4-0.5	218
0.5-0.6	158
0.6-0.7	147
0.7-0.8	38
0.8-0.85	2
0.85-0.9	1
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