NPASS Compound

Structure

NPC11978 OpenBabel06302215222D 44 47 0 0 1 0 0 0 0 0999 V2000 -5.0878 -1.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5878 -2.5411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0878 -3.4071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0878 -3.4071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5878 -2.5411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5878 -2.5411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0878 -1.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0878 -1.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.0878 0.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.5878 0.9230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.0878 0.0570 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -12.6756 -0.7520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.6266 -0.4430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.4927 -0.9430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.9927 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.9927 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -15.3587 -0.4430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -15.3587 0.5570 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -14.4927 1.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.6266 0.5570 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -14.0334 1.4706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.6756 0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -16.2247 1.0570 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5878 -2.5411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0878 -1.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0878 -1.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0878 0.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3171 -2.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3171 -2.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8171 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3578 0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 27 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 14 12 1 1 0 0 0 14 15 1 0 0 0 0 14 25 1 0 0 0 0 15 16 2 0 0 0 0 16 23 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 17 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 26 1 6 0 0 0 22 23 1 0 0 0 0 23 24 1 6 0 0 0 23 25 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 30 31 1 0 0 0 0 32 30 1 6 0 0 0 32 33 1 0 0 0 0 32 43 1 0 0 0 0 33 34 2 0 0 0 0 34 41 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 35 37 1 0 0 0 0 35 38 1 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 39 44 1 1 0 0 0 40 41 1 0 0 0 0 41 42 1 1 0 0 0 41 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	600.42
Volume:	677.603
LogP:	5.174
LogD:	3.295
LogS:	-5.317
# Rotatable Bonds:	8
TPSA:	58.92
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.216
Synthetic Accessibility Score:	5.697
Fsp3:	0.55
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.341
MDCK Permeability:	1.930896360136103e-05
Pgp-inhibitor:	0.899
Pgp-substrate:	0.895
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.131
30% Bioavailability (F30%):	0.019

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.056
Plasma Protein Binding (PPB):	99.42083740234375%
Volume Distribution (VD):	2.345
Pgp-substrate:	5.025899887084961%

ADMET: Metabolism

CYP1A2-inhibitor:	0.066
CYP1A2-substrate:	0.942
CYP2C19-inhibitor:	0.89
CYP2C19-substrate:	0.94
CYP2C9-inhibitor:	0.648
CYP2C9-substrate:	0.995
CYP2D6-inhibitor:	0.929
CYP2D6-substrate:	0.945
CYP3A4-inhibitor:	0.975
CYP3A4-substrate:	0.912

ADMET: Excretion

Clearance (CL):	1.185
Half-life (T1/2):	0.031

ADMET: Toxicity

hERG Blockers:	0.013
Human Hepatotoxicity (H-HT):	0.704
Drug-inuced Liver Injury (DILI):	0.256
AMES Toxicity:	0.056
Rat Oral Acute Toxicity:	0.23
Maximum Recommended Daily Dose:	0.982
Skin Sensitization:	0.103
Carcinogencity:	0.014
Eye Corrosion:	0.003
Eye Irritation:	0.096
Respiratory Toxicity:	0.866

Download Data

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

Natural Product: NPC11978

Natural Product ID:	NPC11978
*Common Name:**	YLUSVJDFTAATNS-NXPBQRLPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YLUSVJDFTAATNS-NXPBQRLPSA-N
Standard InCHI:	InChI=1S/C40H56O4/c1-27(17-13-19-29(3)33-21-35-37(5,6)23-31(41)25-39(35,9)43-33)15-11-12-16-28(2)18-14-20-30(4)34-22-36-38(7,8)24-32(42)26-40(36,10)44-34/h11-22,31-34,41-42H,23-26H2,1-10H3/b12-11+,17-13+,18-14+,27-15+,28-16+,29-19+,30-20+/t31-,32-,33+,34+,39+,40+/m0/s1
SMILES:	C/C(=CC=CC=C(/C)C=CC=C(/C)[C@H]1C=C2C(C)(C)C[C@@H](C[C@@]2(C)O1)O)/C=C/C=C(C)/[C@H]1C=C2C(C)(C)C[C@@H](C[C@@]2(C)O1)O
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:0000259] Prenol lipids [CHEMONTID:0001554] Tetraterpenoids

*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
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.1002/elan.200403102]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.1016/j.foodchem.2012.02.124]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[11077184]
NPO6092	Symphyocladia latiuscula	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11141124]
NPO3699	Acacia aulacocarpa	Species	Fabaceae	Eukaryota	n.a.	leaf	n.a.	PMID[11735581]
NPO6092	Symphyocladia latiuscula	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15844965]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[17328234]
NPO6092	Symphyocladia latiuscula	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17602526]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flower buds	n.a.	n.a.	PMID[18321056]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	flower	n.a.	PMID[21804227]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	flower buds	Henan province, China	2005-MAY	PMID[21942812]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	flower bud	n.a.	PMID[21942812]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[23265495]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flower buds	n.a.	n.a.	PMID[24279769]
NPO3853	Aspidosperma subincanum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3853	Aspidosperma subincanum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4823	Psiadia dentata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7569	Guatteria boliviana	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8418	Anemone flaccida	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19948	Neolentinus lepideus	Species	Gloeophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO7569	Guatteria boliviana	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3699	Acacia aulacocarpa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO471	Ardisia neriifolia	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3853	Aspidosperma subincanum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6729	Juniperus brevifolia	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3597	Rheedia acuminata	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6092	Symphyocladia latiuscula	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6237	Cryptocarya aschersoniana	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4823	Psiadia dentata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19948	Neolentinus lepideus	Species	Gloeophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8418	Anemone flaccida	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5155	Peritassa compta	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5196	Eupatorium argentinum	Species	Asteraceae	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 NPC11978 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	177
0.1-0.2	1286
0.2-0.3	4853
0.3-0.4	13031
0.4-0.5	13068
0.5-0.6	8086
0.6-0.7	2053
0.7-0.8	143
0.8-0.85	0
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 NPC11978 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	161
0.1-0.2	1333
0.2-0.3	4222
0.3-0.4	2469
0.4-0.5	665
0.5-0.6	240
0.6-0.7	47
0.7-0.8	13
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