NPASS Compound

Structure

NPC173069 OpenBabel06302215402D 27 29 0 0 1 0 0 0 0 0999 V2000 -3.5192 0.1997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3852 0.6997 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2512 0.1997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1172 0.6997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1172 1.6997 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.2512 2.1997 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.2512 3.1997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3852 1.6997 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2807 2.6943 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3025 2.9022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8025 2.0361 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4716 1.2930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8080 1.9316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8944 2.3384 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7035 2.9261 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4013 1.0181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4067 0.9135 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1810 1.7226 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1756 1.6180 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5823 0.7045 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9945 -0.1045 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4013 -1.0181 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 2.5768 0.6000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7634 2.4271 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2257 2.6361 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9833 2.1997 0.0000 O 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 8 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 27 1 1 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 8 12 1 1 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 13 1 1 0 0 0 13 14 1 0 0 0 0 13 15 1 0 0 0 0 13 16 1 0 0 0 0 17 16 1 1 0 0 0 17 18 1 0 0 0 0 17 23 1 0 0 0 0 18 19 1 0 0 0 0 18 26 1 6 0 0 0 19 20 1 0 0 0 0 19 25 1 1 0 0 0 20 21 1 0 0 0 0 20 24 1 1 0 0 0 21 22 1 1 0 0 0 21 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	386.27
Volume:	398.844
LogP:	2.902
LogD:	2.668
LogS:	-3.339
# Rotatable Bonds:	3
TPSA:	99.38
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.591
Synthetic Accessibility Score:	5.361
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.121
MDCK Permeability:	2.3929094822960906e-05
Pgp-inhibitor:	0.04
Pgp-substrate:	0.992
Human Intestinal Absorption (HIA):	0.016
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.13

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.03
Plasma Protein Binding (PPB):	88.0776596069336%
Volume Distribution (VD):	0.857
Pgp-substrate:	8.488884925842285%

ADMET: Metabolism

CYP1A2-inhibitor:	0.019
CYP1A2-substrate:	0.513
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.858
CYP2C9-inhibitor:	0.01
CYP2C9-substrate:	0.142
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.24
CYP3A4-inhibitor:	0.04
CYP3A4-substrate:	0.098

ADMET: Excretion

Clearance (CL):	2.28
Half-life (T1/2):	0.547

ADMET: Toxicity

hERG Blockers:	0.171
Human Hepatotoxicity (H-HT):	0.245
Drug-inuced Liver Injury (DILI):	0.089
AMES Toxicity:	0.043
Rat Oral Acute Toxicity:	0.057
Maximum Recommended Daily Dose:	0.032
Skin Sensitization:	0.509
Carcinogencity:	0.057
Eye Corrosion:	0.014
Eye Irritation:	0.153
Respiratory Toxicity:	0.967

Download Data

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

Natural Product: NPC173069

Natural Product ID:	NPC173069
*Common Name:**	YVYUFXNUBVUJMU-QXLPULITSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YVYUFXNUBVUJMU-QXLPULITSA-N
Standard InCHI:	InChI=1S/C21H38O6/c1-11-6-7-15(22)12(2)21(11)9-8-14(10-21)20(4,5)27-19-18(25)17(24)16(23)13(3)26-19/h11-19,22-25H,6-10H2,1-5H3/t11-,12-,13+,14+,15+,16-,17-,18+,19-,21-/m0/s1
SMILES:	C[C@H]1CC[C@H]([C@H](C)[C@@]21CC[C@H](C2)C(C)(C)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](C)O1)O)O)O)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:0002049] Terpene glycosides

*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
NPO14306	Brackenridgea nitida	Species	Ochnaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11076551]
NPO18723	Zanthoxylum avicennae	Species	Rutaceae	Eukaryota	stem wood	Pakuashan, Changhua County, Taiwan	2006-Jun	PMID[18211005]
NPO16952	Asclepias syriaca	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22316168]
NPO19201	Populus alba	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16952	Asclepias syriaca	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18723	Zanthoxylum avicennae	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18723	Zanthoxylum avicennae	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16952	Asclepias syriaca	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19201	Populus alba	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16952	Asclepias syriaca	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18723	Zanthoxylum avicennae	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16952	Asclepias syriaca	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27584	Xylopia frutescens	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14306	Brackenridgea nitida	Species	Ochnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18948	Penicillium decumbens	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19454	Clausena euchrestifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12865	Asperula tinctoria	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19312	Agnorhiza reticulata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19324	Nephroma cellulosum	Species	Nephromataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18723	Zanthoxylum avicennae	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19201	Populus alba	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5438	Ficus racemosa	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12917	Eria elegans	Species	Orchidaceae	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 NPC173069 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	403
0.1-0.2	3934
0.2-0.3	11674
0.3-0.4	11809
0.4-0.5	6041
0.5-0.6	5118
0.6-0.7	2887
0.7-0.8	757
0.8-0.85	57
0.85-0.9	15
0.9-0.95	2
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 NPC173069 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	420
0.1-0.2	4127
0.2-0.3	3126
0.3-0.4	808
0.4-0.5	328
0.5-0.6	266
0.6-0.7	69
0.7-0.8	6
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