NPASS Compound

Structure

NPC96471 OpenBabel06302215222D 23 25 0 0 1 0 0 0 0 0999 V2000 2.0908 0.7247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1248 0.4659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6594 -1.1088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 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 -1.7321 0.0000 0.0000 C 0 0 0 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 -2.5981 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 1 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 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.9641 -1.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9641 -1.1340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9641 -2.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9641 -2.8660 0.0000 C 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 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 23 1 0 0 0 0 3 4 1 6 0 0 0 3 5 1 0 0 0 0 5 6 1 0 0 0 0 7 6 1 6 0 0 0 7 8 1 0 0 0 0 7 12 1 0 0 0 0 8 9 2 0 0 0 0 8 23 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 17 1 0 0 0 0 12 13 1 6 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 6 0 0 0 17 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	316.24
Volume:	355.774
LogP:	4.995
LogD:	4.289
LogS:	-5.192
# Rotatable Bonds:	3
TPSA:	26.3
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.511
Synthetic Accessibility Score:	4.435
Fsp3:	0.762
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.738
MDCK Permeability:	3.0832950869807974e-05
Pgp-inhibitor:	0.011
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.929
30% Bioavailability (F30%):	0.542

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.046
Plasma Protein Binding (PPB):	95.0501937866211%
Volume Distribution (VD):	1.012
Pgp-substrate:	4.195692539215088%

ADMET: Metabolism

CYP1A2-inhibitor:	0.163
CYP1A2-substrate:	0.583
CYP2C19-inhibitor:	0.291
CYP2C19-substrate:	0.902
CYP2C9-inhibitor:	0.318
CYP2C9-substrate:	0.48
CYP2D6-inhibitor:	0.434
CYP2D6-substrate:	0.424
CYP3A4-inhibitor:	0.952
CYP3A4-substrate:	0.399

ADMET: Excretion

Clearance (CL):	3.77
Half-life (T1/2):	0.165

ADMET: Toxicity

hERG Blockers:	0.012
Human Hepatotoxicity (H-HT):	0.167
Drug-inuced Liver Injury (DILI):	0.042
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.019
Maximum Recommended Daily Dose:	0.821
Skin Sensitization:	0.297
Carcinogencity:	0.096
Eye Corrosion:	0.045
Eye Irritation:	0.665
Respiratory Toxicity:	0.92

Download Data

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

Natural Product: NPC96471

Natural Product ID:	NPC96471
*Common Name:**	QMZKBAQNFAMESG-GBMAXXPESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QMZKBAQNFAMESG-GBMAXXPESA-N
Standard InCHI:	InChI=1S/C21H32O2/c1-6-19(2)13-10-16-15(14-19)8-9-17-20(16,3)11-7-12-21(17,4)18(22)23-5/h6,8,16-17H,1,7,9-14H2,2-5H3/t16-,17+,19-,20+,21+/m0/s1
SMILES:	C=C[C@@]1(C)CC[C@H]2C(=CC[C@@H]3[C@]2(C)CCC[C@@]3(C)C(=O)OC)C1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	3032412
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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
NPO25880	Sarcococca coriacea	Species	Buxaceae	Eukaryota	leaves	Nepalese	n.a.	PMID[11421762]
NPO9829	Arnica chamissonis	Species	Asteraceae	Eukaryota	n.a.	rhizome	n.a.	PMID[16644542]
NPO9829	Arnica chamissonis	Species	Asteraceae	Eukaryota	n.a.	root	n.a.	PMID[16644542]
NPO9829	Arnica chamissonis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23501116]
NPO24299	Litsea laurifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24299	Litsea laurifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25483	Croton cortesianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24568	Spongia zimocca	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26279	Premna schimperi	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9829	Arnica chamissonis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26582	Erigeron sumatrensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26464	Macaranga indica	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26799	Vitis heyneana	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25880	Sarcococca coriacea	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25421	Stemodia viscosa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6851	Aplysilla pallida	Species	Darwinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10310	Cutaneotrichosporon cutaneum	Species	Trichosporonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24299	Litsea laurifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20800	Pholiota nameko	Species	Strophariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6478	Tubifera ferruginosa	Species	Reticulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24479	Phaseolus atropurpureus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17593.1	Pinus sylvestris var. hamata	Varieties	Pinaceae	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 NPC96471 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	197
0.1-0.2	1234
0.2-0.3	5939
0.3-0.4	16501
0.4-0.5	7665
0.5-0.6	6186
0.6-0.7	3670
0.7-0.8	1178
0.8-0.85	95
0.85-0.9	19
0.9-0.95	12
0.95-1	1

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 NPC96471 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	186
0.1-0.2	1498
0.2-0.3	4091
0.3-0.4	2272
0.4-0.5	628
0.5-0.6	262
0.6-0.7	145
0.7-0.8	58
0.8-0.85	10
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