NPASS Compound

Structure

NPC188639 OpenBabel06302215172D 43 49 0 0 1 0 0 0 0 0999 V2000 0.0015 -1.7550 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5059 -0.8779 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5191 -0.8788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0265 -0.0018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5207 0.8762 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4921 0.9774 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.1695 0.2238 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6961 1.9327 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8506 2.4218 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8509 3.3989 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5433 3.3984 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3902 3.8871 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3905 4.8648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2374 5.3535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0840 4.8643 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9304 5.3530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7764 4.8639 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.7762 3.8861 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9298 3.3975 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0838 3.8866 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0835 2.8779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2368 3.3980 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2366 2.4208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3896 1.9322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5430 2.4213 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5427 1.4126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9295 2.4202 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5833 1.6938 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.2810 0.7644 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.9347 0.0380 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.8907 0.2409 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.1929 1.1702 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.1489 1.3732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.8026 0.6467 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5392 1.8967 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.5444 -0.4855 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6325 -0.8914 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3250 0.5615 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6420 3.3859 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6427 5.3635 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1242 1.7688 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5074 0.8771 0.0000 O 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 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 43 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 1 0 0 0 5 41 1 0 0 0 0 5 6 1 0 0 0 0 5 42 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 25 1 0 0 0 0 9 10 1 1 0 0 0 9 41 1 0 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 25 1 0 0 0 0 12 13 1 6 0 0 0 12 22 1 0 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 20 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 40 1 6 0 0 0 18 19 1 0 0 0 0 18 39 1 0 0 0 0 19 20 1 0 0 0 0 19 27 1 1 0 0 0 20 21 1 6 0 0 0 20 22 1 0 0 0 0 22 23 1 6 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 1 0 0 0 28 27 1 6 0 0 0 28 29 1 0 0 0 0 28 35 1 0 0 0 0 29 30 1 0 0 0 0 29 38 1 1 0 0 0 30 31 1 0 0 0 0 30 37 1 6 0 0 0 31 32 1 0 0 0 0 31 36 1 1 0 0 0 32 33 1 6 0 0 0 32 35 1 0 0 0 0 33 34 1 0 0 0 0 42 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	610.37
Volume:	607.331
LogP:	3.649
LogD:	3.68
LogS:	-4.065
# Rotatable Bonds:	3
TPSA:	158.3
# H-Bond Aceptor:	10
# H-Bond Donor:	6
# Rings:	7
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.277
Synthetic Accessibility Score:	6.014
Fsp3:	1.0
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
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:	-5.541
MDCK Permeability:	0.0001112358077079989
Pgp-inhibitor:	0.993
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.789
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.742

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.043
Plasma Protein Binding (PPB):	63.49939727783203%
Volume Distribution (VD):	0.396
Pgp-substrate:	7.973066806793213%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.398
CYP2C19-inhibitor:	0.004
CYP2C19-substrate:	0.217
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.024
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.081
CYP3A4-inhibitor:	0.019
CYP3A4-substrate:	0.062

ADMET: Excretion

Clearance (CL):	2.48
Half-life (T1/2):	0.732

ADMET: Toxicity

hERG Blockers:	0.825
Human Hepatotoxicity (H-HT):	0.246
Drug-inuced Liver Injury (DILI):	0.16
AMES Toxicity:	0.134
Rat Oral Acute Toxicity:	0.162
Maximum Recommended Daily Dose:	0.017
Skin Sensitization:	0.949
Carcinogencity:	0.146
Eye Corrosion:	0.008
Eye Irritation:	0.02
Respiratory Toxicity:	0.976

Download Data

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

Natural Product: NPC188639

Natural Product ID:	NPC188639
*Common Name:**	WBEGQJNBXSJMCJ-FAQLCTOPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WBEGQJNBXSJMCJ-FAQLCTOPSA-N
Standard InCHI:	InChI=1S/C33H54O10/c1-15-7-10-33(40-14-15)16(2)24-22(43-33)12-20-18-6-5-17-11-21(35)25(36)29(32(17,4)19(18)8-9-31(20,24)3)42-30-28(39)27(38)26(37)23(13-34)41-30/h15-30,34-39H,5-14H2,1-4H3/t15-,16+,17-,18-,19-,20-,21+,22+,23-,24+,25-,26-,27+,28-,29-,30+,31+,32-,33-/m0/s1
SMILES:	C[C@H]1CC[C@]2([C@H](C)[C@@H]3[C@@H](C[C@H]4[C@H]5CC[C@H]6C[C@H]([C@@H]([C@@H]([C@]6(C)[C@H]5CC[C@@]34C)O[C@@H]3[C@H]([C@@H]([C@H]([C@H](CO)O3)O)O)O)O)O)O2)OC1
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:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides [CHEMONTID:0002364] Steroidal saponins

*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
NPO22018	Hydrangea chinensis	Species	Hydrangeaceae	Eukaryota	Roots	n.a.	n.a.	PMID[11473431]
NPO20244	Melicope semecarpifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11575945]
NPO20244	Melicope semecarpifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18163582]
NPO26918	Taricha granulosa	Species	Salamandridae	Eukaryota	n.a.	n.a.	n.a.	PMID[32896120]
NPO22018	Hydrangea chinensis	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20244	Melicope semecarpifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22018	Hydrangea chinensis	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20244	Melicope semecarpifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23067	Shorea maranti	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14902	Pteris marginata	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16398	Nicotiana alata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1463	Corethrodendron scoparium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20565	Aplysina fulva	Species	Aplysinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22402	Lupinus mutabilis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22018	Hydrangea chinensis	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20244	Melicope semecarpifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22836	Alpinia mutica	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23001	Halimium umbellatum	Species	Cistaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18364	Genista lusitanica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12967	Reseda suffruticosa	Species	Resedaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17338	Solanum asperum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19482	Tapinoma nigerrimum	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20402	Ageratina gilbertii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14627	Caloscypha fulgens	Species	Caloscyphaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26918	Taricha granulosa	Species	Salamandridae	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 NPC188639 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	600
0.1-0.2	5207
0.2-0.3	13714
0.3-0.4	10749
0.4-0.5	5498
0.5-0.6	3522
0.6-0.7	1986
0.7-0.8	939
0.8-0.85	227
0.85-0.9	106
0.9-0.95	52
0.95-1	97

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 NPC188639 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	572
0.1-0.2	4692
0.2-0.3	2743
0.3-0.4	606
0.4-0.5	325
0.5-0.6	166
0.6-0.7	28
0.7-0.8	15
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	1

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